大基因组数据与生物信息学英文及翻译
生物信息学英文术语及释义总汇
Abstract Syntax Notation (ASN.l)（NCBI发展的许多程序，如显示蛋白质三维结构的Cn3D 等所使用的内部格式）A language that is used to describe structured data types formally, Within bioinformatits,it has been used by the National Center for Biotechnology Information to encode sequences, maps, taxonomic information, molecular structures, and biographical information in such a way that it can be easily accessed and exchanged by computer software.Accession number（记录号）A unique identifier that is assigned to a single database entry for a DNA or protein sequence.Affine gap penalty（一种设置空位罚分策略）A gap penalty score that is a linear function of gap length, consisting of a gap opening penalty and a gap extension penalty multiplied by the length of the gap. Using this penalty scheme greatly enhances the performance of dynamic programming methods for sequence alignment. See also Gap penalty.Algorithm（算法）A systematic procedure for solving a problem in a finite number of steps, typically involving a repetition of operations. Once specified, an algorithm can be written in a computer language and run as a program.Alignment（联配/比对/联配）Refers to the procedure of comparing two or more sequences by looking for a series of individual characters or character patterns that are in the same order in the sequences. Of the two types of alignment, local and global, a local alignment is generally the most useful. See also Local and Global alignments.Alignment score（联配/比对/联配值）An algorithmically computed score based on the number of matches, substitutions, insertions, and deletions (gaps) within an alignment. Scores for matches and substitutions Are derived from a scoring matrix such as the BLOSUM and PAM matrices for proteins, and aftine gap penalties suitable for the matrix are chosen. Alignment scores are in log odds units, often bit units (log to the base 2). Higher scores denote better alignments. See also Similarity score, Distance in sequence analysis.Alphabet（字母表）The total number of symbols in a sequence-4 for DNA sequences and 20 for protein sequences.Annotation（注释）The prediction of genes in a genome, including the location of protein-encoding genes, the sequence of the encoded proteins, anysignificantmatches to other Proteins of known function, and the location of RNA-encoding genes. Predictions are based on gene models; e.g., hidden Markov models of introns and exons in proteins encoding genes, and models of secondary structure in RNA.Anonymous FTP（匿名FTP）When a FTP service allows anyone to log in, it is said to provide anonymous FTP ser-vice. A user can log in to an anonymous FTP server by typing anonymous as the user name and his E-mail address as a password. Most Web browsers now negotiate anonymous FTP logon without asking the user for a user name and password. See also FTP.ASCIIThe American Standard Code for Information Interchange (ASCII) encodes unaccented letters a-z, A-Z, the numbers O-9, most punctuation marks, space, and a set of control characters such as carriage return and tab. ASCII specifies 128 characters that are mapped to the values O-127. ASCII tiles are commonly called plain text, meaning that they only encode text without extra markup.BAC clone（细菌人工染色体克隆）Bacterial artificial chromosome vector carrying a genomic DNA insert, typically 100–200 kb. Most of the large-insert clones sequenced in the project were BAC clones.Back-propagation（反向传输）When training feed-forward neural networks, a back-propagation algorithm can be used to modify the network weights. After each training input pattern is fed through the network, the network’s output is compared with the desired output and the amount of error is calculated. This error is back-propagated through the network by using an error function to correct the network weights. See also Feed-forward neural network.Baum-Welch algorithm（Baum-Welch算法）An expectation maximization algorithm that is used to train hidden Markov models.Baye’s rule（贝叶斯法则）Forms the basis of conditional probability by calculating the likelihood of an event occurring based on the history of the event and relevant background information. In terms of two parameters A and B, the theorem is stated in an equation: The condition-al probability of A, given B, P(AIB), is equal to the probability of A, P(A), times the conditional probability of B, given A, P(BIA), divided by the probability of B, P(B). P(A) is the historical or prior distribution value of A, P(BIA) is a new prediction for B for a particular value of A, and P(B) is the sum of the newly predicted values for B. P(AIB) is a posterior probability, representing a new prediction for A given the prior knowledge of A and the newly discovered relationships between A and B.Bayesian analysis（贝叶斯分析）A statistical procedure used to estimate parameters of an underlyingdistribution based on an observed distribution. See also Baye’s rule.Biochips（生物芯片）Miniaturized arrays of large numbers of molecular substrates, often oligonucleotides, in a defined pattern. They are also called DNA microarrays and microchips.Bioinformatics （生物信息学）The merger of biotechnology and information technology with the goal of revealing new insights and principles in biology. /The discipline of obtaining information about genomic or protein sequence data. This may involve similarity searches of databases, comparing your unidentified sequence to the sequences in a database, or making predictions about the sequence based on current knowledge of similar sequences. Databases are frequently made publically available through the Internet, or locally at your institution.Bit score （二进制值/ Bit值）The value S' is derived from the raw alignment score S in which the statistical properties of the scoring system used have been taken into account. Because bit scores have been normalized with respect to the scoring system, they can be used to compare alignment scores from different searches.Bit unitsFrom information theory, a bit denotes the amount of information required to distinguish between two equally likely possibilities. The number of bits of information, AJ, required to convey a message that has A4 possibilities is log2 M = N bits.BLAST （基本局部联配搜索工具，一种主要数据库搜索程序）Basic Local Alignment Search Tool. A set of programs, used to perform fast similarity searches. Nucleotide sequences can be compared with nucleotide sequences in a database using BLASTN, for example. Complex statistics are applied to judge the significance of each match. Reported sequences may be homologous to, or related to the query sequence. The BLASTP program is used to search a protein database for a match against a query protein sequence. There are several other flavours of BLAST. BLAST2 is a newer release of BLAST. Allows for insertions or deletions in the sequences being aligned. Gapped alignments may be more biologically significant.Block（蛋白质家族中保守区域的组块）Conserved ungapped patterns approximately 3-60 amino acids in length in a set of related proteins.BLOSUM matrices（模块替换矩阵，一种主要替换矩阵）An alternative to PAM tables, BLOSUM tables were derived using local multiple alignments of more distantly related sequences than were used for the PAM matrix. These are used to assess thesimilarity of sequences when performing alignments.Boltzmann distribution（Boltzmann 分布）Describes the number of molecules that have energies above a certain level, based on the Boltzmann gas constant and the absolute temperature.Boltzmann probability function(Boltzmann 概率函数)See Boltzmann distribution.Bootstrap analysisA method for testing how well a particular data set fits a model. For example, the validity of the branch arrangement in a predicted phylogenetic tree can be tested by resampling columns in a multiple sequence alignment to create many new alignments. The appearance of a particular branch in trees generated from these resampled sequences can then be measured. Alternatively, a sequence may be left out of an analysis to deter-mine how much the sequence influences the results of an analysis.Branch length（分支长度）In sequence analysis, the number of sequence changes along a particular branch of a phylogenetic tree.CDS or cds （编码序列）Coding sequence.Chebyshe, d inequalityThe probability that a random variable exceeds its mean is less than or equal to the square of 1 over the number of standard deviations from the mean.Clone （克隆）Population of identical cells or molecules (e.g. DNA), derived from a single ancestor.Cloning Vector （克隆载体）A molecule that carries a foreign gene into a host, and allows/facilitates the multiplication of that gene in a host. When sequencing a gene that has been cloned using a cloning vector (rather than by PCR), care should be taken not to include the cloning vector sequence when performing similarity searches. Plasmids, cosmids, phagemids, YACs and PACs are example types of cloning vectors.Cluster analysis（聚类分析）A method for grouping together a set of objects that are most similar from a larger group of related objects. The relationships are based on some criterion of similarity or difference. For sequences, a similarity or distance score or a statistical evaluation of those scores is used.CobblerA single sequence that represents the most conserved regions in a multiple sequence alignment. The BLOCKS server uses the cobbler sequence to perform a database similarity search as a way to reach sequences that are more divergent than would be found using the single sequences in the alignment for searches.Coding system (neural networks)Regarding neural networks, a coding system needs to be designed for representing input and output. The level of success found when training the model will be partially dependent on the quality of the coding system chosen.Codon usageAnalysis of the codons used in a particular gene or organism.COG（直系同源簇）Clusters of orthologous groups in a set of groups of related sequences in microorganism and yeast (S. cerevisiae). These groups are found by whole proteome comparisons and include orthologs and paralogs. See also Orthologs and Paralogs.Comparative genomics（比较基因组学）A comparison of gene numbers, gene locations, and biological functions of genes in the genomes of diverse organisms, one objective being to identify groups of genes that play a unique biological role in a particular organism.Complexity (of an algorithm)（算法的复杂性）Describes the number of steps required by the algorithm to solve a problem as a function of the amount of data; for example, the length of sequences to be aligned.Conditional probability（条件概率）The probability of a particular result (or of a particular value of a variable) given one or more events or conditions (or values of other variables).Conservation （保守）Changes at a specific position of an amino acid or (less commonly, DNA) sequence that preserve the physico-chemical properties of the original residue.Consensus（一致序列）A single sequence that represents, at each subsequent position, the variation found within corresponding columns of a multiple sequence alignment.Context-free grammarsA recursive set of production rules for generating patterns of strings. These consist of a set of terminal characters that are used to create strings, a set of nonterminal symbols that correspond to rules and act as placeholders for patterns that can be generated using terminal characters, a set of rules for replacing nonterminal symbols with terminal characters, and a start symbol.Contig （序列重叠群/拼接序列）A set of clones that can be assembled into a linear order. A DNA sequence that overlaps with another contig. The full set of overlapping sequences (contigs) can be put together to obtain the sequence for a long region of DNA that cannot be sequenced in one run in a sequencing assay. Important in genetic mapping at the molecular level.CORBA（国际对象管理协作组制定的使OOP对象与网络接口统一起来的一套跨计算机、操作系统、程序语言和网络的共同标准）The Common Object Request Broker Architecture (CORBA) is an open industry standard for working with distributed objects, developed by the Object Management Group. CORBA allows the interconnection of objects and applications regardless of computer language, machine architecture, or geographic location of the computers.Correlation coefficient（相关系数）A numerical measure, falling between - 1 and 1, of the degree of the linear relationship between two variables. A positive value indicates a direct relationship, a negative value indicates an inverse relationship, and the distance of the value away from zero indicates the strength of the relationship. A value near zero indicates no relationship between the variables.Covariation (in sequences)（共变）Coincident change at two or more sequence positions in related sequences that may influence the secondary structures of RNA or protein molecules.Coverage (or depth) （覆盖率/厚度）The average number of times a nucleotide is represented by a high-quality base in a collection of random raw sequence. Operationally, a 'high-quality base' is defined as one with an accuracy of at least 99% (corresponding to a PHRED score of at least 20).Database（数据库）A computerized storehouse of data that provides a standardized way for locating, adding, removing, and changing data. See also Object-oriented database, Relational database.DendogramA form of a tree that lists the compared objects (e.g., sequences or genes in a microarray analysis) in a vertical order and joins related ones by levels of branches extending to one side of the list.Depth （厚度）See coverageDirichlet mixturesDefined as the conjugational prior of a multinomial distribution. One use is for predicting the expected pattern of amino acid variation found in the match state of a hid-den Markov model (representing one column of a multiple sequence alignment of proteins), based on prior distributions found in conserved protein domains (blocks).Distance in sequence analysis（序列距离）The number of observed changes in an optimal alignment of two sequences, usually not counting gaps.DNA Sequencing （DNA测序）The experimental process of determining the nucleotide sequence of a region of DNA. This is done by labelling each nucleotide (A, C, G or T) with either a radioactive or fluorescent marker which identifies it. There are several methods of applying this technology, each with their advantages and disadvantages. For more information, refer to a current text book. High throughput laboratories frequently use automated sequencers, which are capable of rapidly reading large numbers of templates. Sometimes, the sequences may be generated more quickly than they can be characterised.Domain （功能域）A discrete portion of a protein assumed to fold independently of the rest of the protein andpossessing its own function.Dot matrix（点标矩阵图）Dot matrix diagrams provide a graphical method for comparing two sequences. One sequence is written horizontally across the top of the graph and the other along the left-hand side. Dots are placed within the graph at the intersection of the same letter appearing in both sequences. A series of diagonal lines in the graph indicate regions of alignment. The matrix may be filtered to reveal the most-alike regions by scoring a minimal threshold number of matches within a sequence window.Draft genome sequence （基因组序列草图）The sequence produced by combining the information from the individual sequenced clones (by creating merged sequence contigs and then employing linking information to create scaffolds) and positioning the sequence along the physical map of the chromosomes.DUST （一种低复杂性区段过滤程序）A program for filtering low complexity regions from nucleic acid sequences.Dynamic programming（动态规划法）A dynamic programming algorithm solves a problem by combining solutions to sub-problems that are computed once and saved in a table or matrix. Dynamic programming is typically used when a problem has many possible solutions and an optimal one needs to be found. This algorithm is used for producing sequence alignments, given a scoring system for sequence comparisons.EMBL （欧洲分子生物学实验室，EMBL数据库是主要公共核酸序列数据库之一）European Molecular Biology Laboratories. Maintain the EMBL database, one of the major public sequence databases.EMBnet （欧洲分子生物学网络）European Molecular Biology Network: /was established in 1988, and provides services including local molecular databases and software for molecular biologists in Europe. There are several large outposts of EMBnet, including EXPASY.Entropy（熵）From information theory, a measure of the unpredictable nature of a set of possible elements. The higher the level of variation within the set, the higher the entropy.Erdos and Renyi lawIn a toss of a “fair” coin, the number of heads in a row that can be expected is the logarithm of the number of tosses to the base 2. The law may be generalized for more than two possible outcomes by changing the base of the logarithm to the number of out-comes. This law was used to analyze the number of matches and mismatches that can be expected between random sequences as a basis for scoring the statistical significance of a sequence alignment.EST （表达序列标签的缩写）See Expressed Sequence TagExpect value (E)（E值）E value. The number of different alignents with scores equivalent to or better than S that are expected to occur in a database search by chance. The lower the E value, the more significant the score. In a database similarity search, the probability that an alignment score as good as the one found between a query sequence and a database sequence would be found in as many comparisons between random sequences as was done to find the matching sequence. In other types of sequence analysis, E has a similar meaning.Expectation maximization (sequence analysis)An algorithm for locating similar sequence patterns in a set of sequences. A guessed alignment of the sequences is first used to generate an expected scoring matrix representing the distribution of sequence characters in each column of the alignment, this pattern is matched to each sequence, and the scoring matrix values are then updated to maximize the alignment of the matrix to the sequences. The procedure is repeated until there is no further improvement.Exon （外显子）Coding region of DNA. See CDS.Expressed Sequence Tag (EST) （表达序列标签）Randomly selected, partial cDNA sequence; represents it's corresponding mRNA. dbEST is a large database of ESTs at GenBank, NCBI.FASTA （一种主要数据库搜索程序）The first widely used algorithm for database similarity searching. The program looks for optimal local alignments by scanning the sequence for small matches called "words". Initially, the scores of segments in which there are multiple word hits are calculated ("init1"). Later the scores of several segments may be summed to generate an "initn" score. An optimized alignment that includes gaps is shown in the output as "opt". The sensitivity and speed of the search are inversely related and controlled by the "k-tup" variable which specifies the size of a "word". (Pearson andLipman)Extreme value distribution（极值分布）Some measurements are found to follow a distribution that has a long tail which decays at high values much more slowly than that found in a normal distribution. This slow-falling type is called the extreme value distribution. The alignment scores between unrelated or random sequences are an example. These scores can reach very high values, particularly when a large number of comparisons are made, as in a database similarity search. The probability of a particular score may be accurately predicted by the extreme value distribution, which follows a double negative exponential function after Gumbel.False negative（假阴性）A negative data point collected in a data set that was incorrectly reported due to a failure of the test in avoiding negative results.False positive （假阳性）A positive data point collected in a data set that was incorrectly reported due to a failure of the test. If the test had correctly measured the data point, the data would have been recorded as negative.Feed-forward neural network （反向传输神经网络）Organizes nodes into sequence layers in which the nodes in each layer are fully connected with the nodes in the next layer, except for the final output layer. Input is fed from the input layer through the layers in sequence in a “feed-forward” direction, resulting in output at the final layer. See also Neural network.Filtering (window size)During pair-wise sequence alignment using the dot matrix method, random matches can be filtered out by using a sliding window to compare the two sequences. Rather than comparing a single sequence position at a time, a window of adjacent positions in the two sequences is compared and a dot, indicating a match, is generated only if a certain minimal number of matches occur.Filtering （过滤）Also known as Masking. The process of hiding regions of (nucleic acid or amino acid) sequence having characteristics that frequently lead to spurious high scores. See SEG and DUST.Finished sequence（完成序列）Complete sequence of a clone or genome, with an accuracy of at least 99.99% and no gaps.Fourier analysisStudies the approximations and decomposition of functions using trigonometric polynomials.Format (file)（格式）Different programs require that information be specified to them in a formal manner, using particular keywords and ordering. This specification is a file format.Forward-backward algorithmUsed to train a hidden Markov model by aligning the model with training sequences. The algorithm then refines the model to reduce the error when fitted to the given data using a gradient descent approach.FTP (File Transfer Protocol)（文件传输协议）Allows a person to transfer files from one computer to another across a network using an FTP-capable client program. The FTP client program can only communicate with machines that run an FTP server. The server, in turn, will make a specific portion of its tile system available for FTP access, providing that the client is able to supply a recognized user name and password to the server.Full shotgun clone （鸟枪法克隆）A large-insert clone for which full shotgun sequence has been produced.Functional genomics（功能基因组学）Assessment of the function of genes identified by between-genome comparisons. The function of a newly identified gene is tested by introducing mutations into the gene and then examining the resultant mutant organism for an altered phenotype.gap （空位/间隙/缺口）A space introduced into an alignment to compensate for insertions and deletions in one sequence relative to another. To prevent the accumulation of too many gaps in an alignment, introduction of a gap causes the deduction of a fixed amount (the gap score) from the alignment score. Extension of the gap to encompass additional nucleotides or amino acid is also penalized in the scoring of an alignment.Gap penalty（空位罚分）A numeric score used in sequence alignment programs to penalize the presence of gaps within an alignment. The value of a gap penalty affects how often gaps appear in alignments produced by the algorithm. Most alignment programs suggest gap penalties that are appropriate for particular scoring matrices.Genetic algorithm（遗传算法）A kind of search algorithm that was inspired by the principles of evolution. A population of initial solutions is encoded and the algorithm searches through these by applying a pre-defined fitness measurement to each solution, selecting those with the highest fitness for reproduction. New solutions can be generated during this phase by crossover and mutation operations, defined in the encoded solutions.Genetic map （遗传图谱）A genome map in which polymorphic loci are positioned relative to one another on the basis of the frequency with which they recombine during meiosis. The unit of distance is centimorgans (cM), denoting a 1% chance of recombination.Genome（基因组）The genetic material of an organism, contained in one haploid set of chromosomes.Gibbs sampling methodAn algorithm for finding conserved patterns within a set of related sequences. A guessed alignment of all but one sequence is made and used to generate a scoring matrix that represents the alignment. The matrix is then matched to the left-out sequence, and a probable location of the corresponding pattern is found. This prediction is then input into a new alignment and another scoring matrix is produced and tested on a new left-out sequence. The process is repeated until there is no further improvement in the matrix.Global alignment（整体联配）Attempts to match as many characters as possible, from end to end, in a set of twomore sequences.Gopher (一个文档发布系统，允许检索和显示文本文件)Graph theory（图论）A branch of mathematics which deals with problems that involve a graph or network structure. A graph is defined by a set of nodes (or points) and a set of arcs (lines or edges) joining the nodes. In sequence and genome analysis, graph theory is used for sequence alignments and clustering alike genes.GSS（基因综述序列）Genome survey sequence.GUI（图形用户界面）Graphical user interface.H （相对熵值）H is the relative entropy of the target and background residue frequencies. (Karlin and Altschul, 1990). H can be thought of as a measure of the average information (in bits) available per position that distinguishes an alignment from chance. At high values of H, short alignments can be distinguished by chance, whereas at lower H values, a longer alignment may be necessary. (Altschul, 1991)Half-bitsSome scoring matrices are in half-bit units. These units are logarithms to the base 2 of odds scores times 2.Heuristic（启发式方法）A procedure that progresses along empirical lines by using rules of thumb to reach a solution. The solution is not guaranteed to be optimal.Hexadecimal system（16制系统）The base 16 counting system that uses the digits O-9 followed by the letters A-F.HGMP （人类基因组图谱计划）Human Genome Mapping Project.Hidden Markov Model (HMM)（隐马尔可夫模型）In sequence analysis, a HMM is usually a probabilistic model of a multiple sequence alignment, but can also be a model of periodic patterns in a single sequence, representing, for example, patterns found in the exons of a gene. In a model of multiple sequence alignments, each column of symbols in the alignment is represented by a frequency distribution of the symbols called a state, and insertions and deletions by other states. One then moves through the model along a particular path from state to state trying to match a given sequence. The next matching symbol is chosen from each state, recording its probability (frequency) and also the probability of going to thatparticular state from a previous one (the transition probability). State and transition probabilities are then multiplied to obtain a probability of the given sequence. Generally speaking, a HMM is a statistical model for an ordered sequence of symbols, acting as a stochastic state machine that generates a symbol each time a transition is made from one state to the next. Transitions betweenstates are specified by transition probabilities.Hidden layer（隐藏层）An inner layer within a neural network that receives its input and sends its output to other layers within the network. One function of the hidden layer is to detect covariation within the input data, such as patterns of amino acid covariation that are associated with a particular type of secondary structure in proteins.Hierarchical clustering（分级聚类）The clustering or grouping of objects based on some single criterion of similarity or difference.An example is the clustering of genes in a microarray experiment based on the correlation between their expression patterns. The distance method used in phylogenetic analysis is another example.Hill climbingA nonoptimal search algorithm that selects the singular best possible solution at a given state or step. The solution may result in a locally best solution that is not a globally best solution.Homology（同源性）A similar component in two organisms (e.g., genes with strongly similar sequences) that can be attributed to a common ancestor of the two organisms during evolution.Horizontal transfer（水平转移）The transfer of genetic material between two distinct species that do not ordinarily exchange genetic material. The transferred DNA becomes established in the recipient genome and can be detected by a novel phylogenetic history and codon content com-pared to the rest of the genome.HSP （高比值片段对）High-scoring segment pair. Local alignments with no gaps that achieve one of the top alignment scores in a given search.HTGS/HGT（高通量基因组序列）High-throughout genome sequences。
大基因组数据与生物信息学英文及翻译
Big Genomic Data in Bioinformatics CloudAbstractThe achievement of Human Genome project has led to the proliferation of genomic sequencing data. This along with the next generation sequencing has helped to reduce the cost of sequencing,which has further increased the demand of analysis of this large genomic data. This data set and its processing has aided medical researches.Thus, we require expertise to deal with biological big data. The concept of cloud computing and big data technologies such as the Apache Hadoop project, are hereby needed to store, handle and analyse this data. Because, these technologies provide distributed and parallelized data processing and are efficient to analyse even petabyte (PB) scale data sets. However, there are some demerits too which may include need of larger time to transfer data and lesser network bandwidth, majorly.人类基因组计划的实现导致基因组测序数据的增殖。
生物信息学术语
生物信息学术语BLAST ：Basic Local Alignment Search Tool，基本的基于局部对准的搜索工具；一种快速查找与给定序列具有连续相同片断的序列的技术。
Entrez ：美国国家生物技术信息中心所提供的在线资源检索器。
该资源将GenBank序列与其原始文献出处链接在一起。
NCBI ：美国国立生物技术信息中心（National Center for Biotechnology Information），1988年设立，为美国国家医学图书馆（NLM）和国家健康协会（NIH）下属部门之一。
提供生物医学领域的信息学服务，如世界三大核酸数据库之一的GenBank数据库，PubMed医学文献检索数据库等。
Conserved sequence ：保守序列。
演化过程中基本上不变的DNA中的碱基序列或蛋白质中的氨基酸序列。
Domain ：功能域。
蛋白质中具有某种特定功能的部分，它在序列上未必是连续的。
某蛋白质中所有功能域组合其起来决定着该蛋白质的全部功能。
EBI：欧洲生物信息学研究所（European Bioinformatics Institute）。
The National Center for Biotechnology Information (NCBI) at the NationalLibrary of Medicine (NLM), National Institutes of Health (NIH)EMBL ：欧洲分子生物学实验室（uropean Molecular Biology Laboratory）。
GenBank ：由美国国家生物技术信息中心提供的核酸序列数据库。
Gene ：基因。
遗传的基本的物理和功能单位。
一个基因就是位于某条染色体的某个位置上的核苷酸序列，其中蕴含着某种特定功能产物（如蛋白质或RNA分子）的编码。
DUST ：A program for filtering low complexity regions from nucleic acid sequences.Gene expression ：基因表达。
生物信息学与基因组学
HGP的意义
诞生了新学科、新领域
生物信息学 比较基因组学(comparative genomics) 以跨物种、跨群体的DNA序列比较为基础，利用模式 生物与人类基因组之间便码顺序和组成、结构上的同 源性，研究物种起源、进化、基因功能演化、差异表 达和定位、克隆人类疾病基因
人类基因组研究方向
基因组学（genomics）作为一门专门学科。它涵盖以下 几个方面： 结构基因组学，主要研究核酸或蛋白质的结构、定位、 功能及其相互作用；与蛋白质组学内容密切相关。 功能基因组学，主要研究基因的表达、调控、功能及 基因间的相互作用； 比较基因组学, 包括对不同进化阶段生物基因组的比 较研究，也包括不同人种、族群和群体基因组的比较研 究。 药物基因组学、疾病基因组学等分支学科也不断发展 起来。
2. 概念：从整体上研究一个物种的所有基因结构和功能的新科 学。
人类基因组计划（HGP）
人类基因组计划的主要目标是测定人类基因组全序列。人 类基因组DNA由四种核苷酸（A、T、C、G）按一定的顺 序排列而成，基因组所含核苷酸总数为30亿对。
４月末 我国科学家按照国际人类基因组计划的部署， 完成 了１％人类基因组的工作框架图。 ５月 国际人类基因组计划完成时间再度提前，预计 从原定 的２００３年６月提前至２００１年６月。 ５月８日 由德国和日本等国科学家组成的国际科研 小组宣 布，他们已经基本完成了人体第２１对染色体的测 序工作。 ６月２６日 各国科学家公布了人类基因组工作草图。 ２００1年 2月15日 公布了人类基因组全序列及其分析结果， 宣告人类有30,000 - 40,000条编码蛋白质的基因, 仅占人类基因 组序列的1％～5％，成人各种组织中又只有约10％的基因表达 为蛋白质。。
生物信息学,英文
生物信息学,英文BioinformaticsBioinformatics is a rapidly growing field that combines biology, computer science, and information technology to analyze and interpret biological data. It has become an essential tool in modern scientific research, particularly in the fields of genomics, proteomics, and molecular biology. The advent of high-throughput sequencing technologies has led to an exponential increase in the amount of biological data available, and bioinformatics provides the means to manage, analyze, and interpret this vast amount of information.At its core, bioinformatics involves the use of computational methods and algorithms to store, retrieve, organize, analyze, and interpret biological data. This includes tasks such as DNA and protein sequence analysis, gene and protein structure prediction, and the identification of functional relationships between different biological molecules. Bioinformatics also plays a crucial role in the development of new drugs, the understanding of disease mechanisms, and the study of evolutionary processes.One of the primary applications of bioinformatics is in the field ofgenomics, where it is used to analyze and interpret DNA sequence data. Researchers can use bioinformatics tools to identify genes, predict their function, and study the genetic variation within and between species. This information is essential for understanding the genetic basis of diseases, developing personalized medicine, and exploring the evolutionary history of different organisms.In addition to genomics, bioinformatics is also widely used in proteomics, the study of the structure and function of proteins. Bioinformatics tools can be used to predict the three-dimensional structure of proteins, identify protein-protein interactions, and study the role of proteins in biological processes. This information is crucial for understanding the mechanisms of disease, developing new drugs, and engineering proteins for industrial and medical applications.Another important application of bioinformatics is in the field of systems biology, which aims to understand the complex interactions and relationships between different biological components within a living organism. By using computational models and simulations, bioinformaticians can study how these components work together to produce the observed behavior of a biological system. This knowledge can be used to develop new treatments for diseases, optimize agricultural practices, and gain a deeper understanding of the fundamental principles of life.Bioinformatics is also playing a crucial role in the field of personalized medicine, where the goal is to tailor medical treatments to the unique genetic and molecular profile of each individual patient. By using bioinformatics tools to analyze a patient's genetic and molecular data, healthcare providers can identify the most effective treatments and predict the likelihood of adverse reactions to certain drugs. This approach has the potential to improve patient outcomes, reduce healthcare costs, and pave the way for more targeted and effective therapies.In addition to its scientific applications, bioinformatics is also having a significant impact on various industries, such as agriculture, environmental science, and forensics. In agriculture, bioinformatics is used to improve crop yields, develop new pest-resistant varieties, and optimize the use of resources. In environmental science, bioinformatics is used to study the impact of human activities on ecosystems, identify new sources of renewable energy, and monitor the health of the planet. In forensics, bioinformatics is used to analyze DNA evidence and identify individuals involved in criminal activities.Despite the many benefits of bioinformatics, there are also significant challenges and ethical considerations that need to be addressed. As the amount of biological data continues to grow, there is an increasing need for efficient data storage, management, andsecurity systems. Additionally, the interpretation of biological data requires a deep understanding of both biological and computational principles, which can be a barrier for some researchers and healthcare providers.Furthermore, the use of bioinformatics in areas such as personalized medicine and forensics raises important ethical questions regarding privacy, informed consent, and the potential for discrimination based on genetic information. It is crucial that the development and application of bioinformatics technologies be guided by strong ethical principles and robust regulatory frameworks to ensure that they are used in a responsible and equitable manner.In conclusion, bioinformatics is a rapidly evolving field that is transforming the way we understand and interact with the biological world. By combining the power of computer science and information technology with the insights of biology, bioinformatics is enabling new discoveries, improving human health, and shaping the future of scientific research. As the field continues to grow and evolve, it will be important for researchers, policymakers, and the public to work together to ensure that the benefits of bioinformatics are realized in a responsible and ethical manner.。
生物信息学名词解释
生物信息学名词解释1、生物信息学:研究大量生物数据复杂关系的学科,其特征就是多学科交叉,以互联网为媒介,数据库为载体。
利用数学知识建立各种数学模型; 利用计算机为工具对实验所得大量生物学数据进行储存、检索、处理及分析,并以生物学知识对结果进行解释。
2、二级数据库:在一级数据库、实验数据与理论分析的基础上针对特定目标衍生而来,就是对生物学知识与信息的进一步的整理。
3、FASTA序列格式:就是将DNA或者蛋白质序列表示为一个带有一些标记的核苷酸或者氨基酸字符串,大于号(>)表示一个新文件的开始,其她无特殊要求。
4、genbank序列格式:就是GenBank 数据库的基本信息单位,就是最为广泛的生物信息学序列格式之一。
该文件格式按域划分为4个部分:第一部分包含整个记录的信息(描述符);第二部分包含注释;第三部分就是引文区,提供了这个记录的科学依据;第四部分就是核苷酸序列本身,以“//”结尾。
5、Entrez检索系统:就是NCBI开发的核心检索系统,集成了NCBI 的各种数据库,具有链接的数据库多,使用方便,能够进行交叉索引等特点。
6、BLAST:基本局部比对搜索工具,用于相似性搜索的工具,对需要进行检索的序列与数据库中的每个序列做相似性比较。
P947、查询序列(query sequence):也称被检索序列,用来在数据库中检索并进行相似性比较的序列。
P988、打分矩阵(scoring matrix):在相似性检索中对序列两两比对的质量评估方法。
包括基于理论(如考虑核酸与氨基酸之间的类似性)与实际进化距离(如PAM)两类方法。
P299、空位(gap):在序列比对时,由于序列长度不同,需要插入一个或几个位点以取得最佳比对结果,这样在其中一序列上产生中断现象,这些中断的位点称为空位。
P2910、空位罚分:空位罚分就是为了补偿插入与缺失对序列相似性的影响,序列中的空位的引入不代表真正的进化事件,所以要对其进行罚分,空位罚分的多少直接影响对比的结果。
生物信息学主要英文术语及释义
生物信息学主要英文术语及释义Abstract Syntax Notation (ASN.l)（NCBI发展的许多程序，如显示蛋白质三维结构的Cn3D 等所使用的内部格式）A language that is used to describe structured data types formally, Within bioinformatits,it has been used by the National Center for Biotechnology Information to encode sequences, maps, taxonomic information, molecular structures, and biographical information in such a way that it can be easily accessed and exchanged by computer software.Accession number（记录号）A unique identifier that is assigned to a single database entry for a DNA or protein sequence.Affine gap penalty（一种设置空位罚分策略）A gap penalty score that is a linear function of gap length, consisting of a gap opening penalty and a gap extension penalty multiplied by the length of the gap. Using this penalty scheme greatly enhances the performance of dynamic programming methods for sequence alignment. See also Gap penalty.Algorithm（算法）A systematic procedure for solving a problem in a finite number of steps, typically involving a repetition of operations. Once specified, an algorithm can be written in a computer language and run as a program.Alignment（联配/比对/联配）Refers to the procedure of comparing two or more sequences by looking for a series of individual characters or character patterns that are in the same order in the sequences. Of the two types of alignment, local and global, a local alignment is generally the most useful. See also Local and Global alignments.Alignment score（联配/比对/联配值）An algorithmically computed score based on the number of matches, substitutions, insertions, and deletions (gaps) within an alignment. Scores for matches and substitutions Are derived from a scoring matrix such as the BLOSUM and PAM matrices for proteins, and aftine gap penalties suitable for the matrix are chosen. Alignment scores are in log odds units, often bit units (log to the base 2). Higher scores denote better alignments. See also Similarity score, Distance in sequence analysis. Alphabet（字母表）The total number of symbols in a sequence-4 for DNA sequences and 20 for protein sequences.Annotation（注释）The prediction of genes in a genome, including the location of protein-encoding genes, the sequence of the encoded proteins, anysignificantmatches to other Proteins of known function, and the location of RNA-encoding genes. Predictions are based on gene models; e.g., hidden Markov models of introns and exons in proteins encoding genes, and models of secondary structure in RNA.Anonymous FTP（匿名FTP）When a FTP service allows anyone to log in, it is said to provide anonymous FTP ser-vice. A user can log in to an anonymous FTP server by typing anonymous as theuser name and his E-mail address as a password. Most Web browsers now negotiate anonymous FTP logon without asking the user for a user name and password. See also FTP.ASCIIThe American Standard Code for Information Interchange (ASCII) encodes unaccented letters a-z, A-Z, the numbers O-9, most punctuation marks, space, and a set of control characters such as carriage return and tab. ASCII specifies 128 characters that are mapped to the value s O-127. ASCII tiles are commonly called plain text, meaning that they only encode text without extra markup.BAC clone（细菌人工染色体克隆）Bacterial artificial chromosome vector carrying a genomic DNA insert, typically 100–200 kb. Most of the large-insert clones sequenced in the project were BAC clones. Back-propagation（反向传输）When training feed-forward neural networks, a back-propagation algorithm can be used to modify the network weights. After each training input pattern is fed through the network, the network’s output is compared with the desired output and the amount of error is calculated. This error is back-propagated through the network by using an error function to correct the network weights. See also Feed-forward neural network.Baum-Welch algorithm（Baum-Welch算法）An expectation maximization algorithm that is used to train hidden Markov models. Baye’s rule（贝叶斯法则）Forms the basis of conditional probability by calculating the likelihood of an event occurring based on the history of the event and relevant background information. In terms of two parameters A and B, the theorem is stated in an equation: The condition-al probability of A, given B, P(AIB), is equal to the probability of A, P(A), times the conditional probability of B, given A, P(BIA), divided by the probability of B, P(B). P(A) is the historical or prior distribution value of A, P(BIA) is a new prediction for B for a particular value of A, and P(B) is the sum of the newly predicted value s for B. P(AIB) is a posterior probability, representing a new prediction for A given the prior knowledge of A and the newly discovered relationships between A and B.Bayesian analysis（贝叶斯分析）A statistical procedure used to estimate parameters of an underlyingdistribution based on an observed distribution. See a lso Baye’s rule.Biochips（生物芯片）Miniaturized arrays of large numbers of molecular substrates, often oligonucleotides, in a defined pattern. They are also called DNA microarrays and microchips.Bioinformatics （生物信息学）The merger of biotechnology and information technology with the goal of revealing new insights and principles in biology. /The discipline of obtaining information about genomic or protein sequence data. This may involve similarity searches of databases, comparing your unidentified sequence to the sequences in a database, ormaking predictions about the sequence based on current knowledge of similar sequences. Databases are frequently made publically available through the Internet, or locally at your institution.Bit score （二进制值/ Bit值）The value S' is derived from the raw alignment score S in which the statistical properties of the scoring system used have been taken into account. Because bit scores have been normalized with respect to the scoring system, they can be used to compare alignment scores from different searches.Bit unitsFrom information theory, a bit denotes the amount of information required to distinguish between two equally likely possibilities. The number of bits of information, AJ, required to convey a message that has A4 possibilities is log2 M = N bits.BLAST （基本局部联配搜索工具，一种主要数据库搜索程序）Basic Local Alignment Search Tool. A set of programs, used to perform fast similarity searches. Nucleotide sequences can be compared with nucleotide sequences in a database using BLASTN, for example. Complex statistics are applied to judge the significance of each match. Reported sequences may be homologous to, or related to the query sequence. The BLASTP program is used to search a protein database for a match against a query protein sequence. There are several other flavours of BLAST. BLAST2 is a newer release of BLAST. Allows for insertions or deletions in the sequences being aligned. Gapped alignments may be more biologically significant. Block（蛋白质家族中保守区域的组块）Conserved ungapped patterns approximately 3-60 amino acids in length in a set of related proteins.BLOSUM matrices（模块替换矩阵，一种主要替换矩阵）An alternative to PAM tables, BLOSUM tables were derived using local multiple alignments of more distantly related sequences than were used for the PAM matrix. These are used to assess the similarity of sequences when performing alignments. Boltzmann distribution（Boltzmann 分布）Describes the number of molecules that have energies above a certain level, based on the Boltzmann gas constant and the absolute temperature.Boltzmann probability function(Boltzmann概率函数)See Boltzmann distribution.Bootstrap analysisA method for testing how well a particular data set fits a model. For example, the validity of the branch arrangement in a predicted phylogenetic tree can be tested by resampling columns in a multiple sequence alignment to create many new alignments. The appearance of a particular branch in trees generated from these resampled sequences can then be measured. Alternatively, a sequence may be left out of an analysis to deter-mine how much the sequence influences the results of an analysis. Branch length（分支长度）In sequence analysis, the number of sequence changes along a particular branch of a phylogenetic tree.CDS or cds （编码序列）Coding sequence.Chebyshe, d inequalityThe probability that a random variable exceeds its mean is less than or equal to the square of 1 over the number of standard deviations from the mean.Clone （克隆）Population of identical cells or molecules (e.g. DNA), derived from a single ancestor. Cloning Vector （克隆载体）A molecule that carries a foreign gene into a host, and allows/facilitates the multiplication of that gene in a host. When sequencing a gene that has been cloned using a cloning vector (rather than by PCR), care should be taken not to include the cloning vector sequence when performing similarity searches. Plasmids, cosmids, phagemids, YACs and PACs are example types of cloning vectors.Cluster analysis（聚类分析）A method for grouping together a set of objects that are most similar from a larger group of related objects. The relationships are based on some criterion of similarity or difference. For sequences, a similarity or distance score or a statistical evaluation of those scores is used.CobblerA single sequence that represents the most conserved regions in a multiple sequence alignment. The BLOCKS server uses the cobbler sequence to perform a database similarity search as a way to reach sequences that are more divergent than would be found using the single sequences in the alignment for searches.Coding system (neural networks)Regarding neural networks, a coding system needs to be designed for representing input and output. The level of success found when training the model will be partially dependent on the quality of the coding system chosen.Codon usageAnalysis of the codons used in a particular gene or organism.COG（直系同源簇）Clusters of orthologous groups in a set of groups of related sequences in microorganism and yeast (S. cerevisiae). These groups are found by whole proteome comparisons and include orthologs and paralogs. See also Orthologs and Paralogs. Comparative genomics（比较基因组学）A comparison of gene numbers, gene locations, and biological functions of genes in the genomes of diverse organisms, one objective being to identify groups of genes that play a unique biological role in a particular organism.Complexity (of an algorithm)（算法的复杂性）Describes the number of steps required by the algorithm to solve a problem as a function of the amount of data; for example, the length of sequences to be aligned. Conditional probability（条件概率）The probability of a particular result (or of a particular value of a variable) given one or more events or conditions (or value s of other variables).Conservation （保守）Changes at a specific position of an amino acid or (less commonly, DNA) sequencethat preserve the physico-chemical properties of the original residue. Consensus（一致序列）A single sequence that represents, at each subsequent position, the variation found within corresponding columns of a multiple sequence alignment.Context-free grammarsA recursive set of production rules for generating patterns of strings. These consist of a set of terminal characters that are used to create strings, a set of nonterminal symbols that correspond to rules and act as placeholders for patterns that can be generated using terminal characters, a set of rules for replacing nonterminal symbols with terminal characters, and a start symbol.Contig （序列重叠群/拼接序列）A set of clones that can be assembled into a linear order. A DNA sequence that overlaps with another contig. The full set of overlapping sequences (contigs) can be put together to obtain the sequence for a long region of DNA that cannot be sequenced in one run in a sequencing assay. Important in genetic mapping at the molecular level. CORBA（国际对象管理协作组制定的使OOP对象与网络接口统一起来的一套跨计算机、操作系统、程序语言和网络的共同标准）The Common Object Request Broker Architecture (CORBA) is an open industry standard for working with distributed objects, developed by the Object Management Group. CORBA allows the interconnection of objects and applications regardless of computer language, machine architecture, or geographic location of the computers. Correlation coefficient（相关系数）A numerical measure, falling between - 1 and 1, of the degree of the linear relationship between two variables. A positive value indicates a direct relationship, a negative value indicates an inverse relationship, and the distance of the value away from zero indicates the strength of the relationship. A value near zero indicates no relationship between the variables. Covariation (in sequences)（共变）Coincident change at two or more sequence positions in related sequences that may influence the secondary structures of RNA or protein molecules.Coverage (or depth) （覆盖率/厚度）The average number of times a nucleotide is represented by a high-quality base in a collection of random raw sequence. Operationally, a 'high-quality base' is defined as one with an accuracy of at least 99% (corresponding to a PHRED score of at least 20).Database（数据库）A computerized storehouse of data that provides a standardized way for locating, adding, removing, and changing data. See also Object-oriented database, Relational database.DendogramA form of a tree that lists the compared objects (e.g., sequences or genes in a microarray analysis) in a vertical order and joins related ones by levels of branches extending to one side of the list.Depth （厚度）See coverageDirichlet mixturesDefined as the conjugational prior of a multinomial distribution. One use is for predicting the expected pattern of amino acid variation found in the match state of a hid-den Markov model (representing one column of a multiple sequence alignment of proteins), based on prior distributions found in conserved protein domains (blocks).Distance in sequence analysis（序列距离）The number of observed changes in an optimal alignment of two sequences, usually not counting gaps.DNA Sequencing （DNA测序）The experimental process of determining the nucleotide sequence of a region of DNA. This is done by labelling each nucleotide (A, C, G or T) with either a radioactive or fluorescent marker which identifies it. There are several methods of applying this technology, each with their advantages and disadvantages. For more information, refer to a current text book. High throughput laboratories frequently use automated sequencers, which are capable of rapidly reading large numbers of templates. Sometimes, the sequences may be generated more quickly than they can be characterised. Domain （功能域）A discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function.Dot matrix（点标矩阵图）Dot matrix diagrams provide a graphical method for comparing two sequences. One sequence is written horizontally across the top of the graph and the other along the left-hand side. Dots are placed within the graph at the intersection of the same letter appearing in both sequences. A series of diagonal lines in the graph indicate regions of alignment. The matrix may be filtered to reveal the most-alike regions by scoring a minimal threshold number of matches within a sequence window.Draft genome sequence （基因组序列草图）The sequence produced by combining the information from the individual sequenced clones (by creating merged sequence contigs and then employing linking information to create scaffolds) and positioning the sequence along the physical map of the chromosomes.DUST （一种低复杂性区段过滤程序）A program for filtering low complexity regions from nucleic acid sequences. Dynamic programming（动态规划法）A dynamic programming algorithm solves a problem by combining solutions to sub-problems that are computed once and saved in a table or matrix. Dynamic programming is typically used when a problem has many possible solutions and an optimal one needs to be found. This algorithm is used for producing sequence alignments, given a scoring system for sequence comparisons.EMBL （欧洲分子生物学实验室，EMBL数据库是主要公共核酸序列数据库之一）European Molecular Biology Laboratories. Maintain the EMBL database, one of the major public sequence databases.EMBnet （欧洲分子生物学网络）European Molecular Biology Network: / was established in 1988,and provides services including local molecular databases and software for molecular biologists in Europe. There are several large outposts of EMBnet, including EXPASY. Entropy（熵）From information theory, a measure of the unpredictable nature of a set of possible elements. The higher the level of variation within the set, the higher the entropy. Erdos and Renyi lawIn a toss of a “fair” coin, the number of heads in a row that can be expected is the logarithm of the number of tosses to the base 2. The law may be generalized for more than two possible outcomes by changing the base of the logarithm to the number of out-comes. This law was used to analyze the number of matches and mismatches that can be expected between random sequences as a basis for scoring the statistical significance of a sequence alignment.EST （表达序列标签的缩写）See Expressed Sequence TagExpect value (E)（E值）E value. The number of different alignents with scores equivalent to or better than S that are expected to occur in a database search by chance. The lower the E value, the more significant the score. In a database similarity search, the probability that an alignment score as good as the one found between a query sequence and a database sequence would be found in as many comparisons between random sequences as was done to find the matching sequence. In other types of sequence analysis, E has a similar meaning.Expectation maximization (sequence analysis)An algorithm for locating similar sequence patterns in a set of sequences. A guessed alignment of the sequences is first used to generate an expected scoring matrix representing the distribution of sequence characters in each column of the alignment, this pattern is matched to each sequence, and the scoring matrix value s are then updated to maximize the alignment of the matrix to the sequences. The procedure is repeated until there is no further improvement.Exon （外显子）Coding region of DNA. See CDS.Expressed Sequence Tag (EST) （表达序列标签）Randomly selected, partial cDNA sequence; represents it's corresponding mRNA. dbEST is a large database of ESTs at GenBank, NCBI.FASTA （一种主要数据库搜索程序）The first widely used algorithm for database similarity searching. The program looks for optimal local alignments by scanning the sequence for small matches called "words". Initially, the scores of segments in which there are multiple word hits are calculated ("init1"). Later the scores of several segments may be summed to generate an "initn" score. An optimized alignment that includes gaps is shown in the output as "opt". The sensitivity and speed of the search are inversely related and controlled by the "k-tup" variable which specifies the size of a "word". (Pearson and Lipman)Extreme value distribution（极值分布）Some measurements are found to follow a distribution that has a long tail which decays at high value s much more slowly than that found in a normal distribution. This slow-falling type is called the extreme value distribution. The alignment scores between unrelated or random sequences are an example. These scores can reach very high value s, particularly when a large number of comparisons are made, as in a database similarity search. The probability of a particular score may be accurately predicted by the extreme value distribution, which follows a double negative exponential function after Gumbel.False negative（假阴性）A negative data point collected in a data set that was incorrectly reported due to a failure of the test in avoiding negative results.False positive （假阳性）A positive data point collected in a data set that was incorrectly reported due to a failure of the test. If the test had correctly measured the data point, the data would have been recorded as negative.Feed-forward neural network （反向传输神经网络）Organizes nodes into sequence layers in which the nodes in each layer are fully connected with the nodes in the next layer, except for the final output layer. Input is fed from the input layer through the layers in sequence in a “feed-forward” direction, resulting in output at the final layer. See also Neural network. Filtering (window size)During pair-wise sequence alignment using the dot matrix method, random matches can be filtered out by using a sliding window to compare the two sequences. Rather than comparing a single sequence position at a time, a window of adjacent positions in the two sequences is compared and a dot, indicating a match, is generated only if a certain minimal number of matches occur.Filtering （过滤）Also known as Masking. The process of hiding regions of (nucleic acid or amino acid) sequence having characteristics that frequently lead to spurious high scores. See SEG and DUST.Finished sequence（完成序列）Complete sequence of a clone or genome, with an accuracy of at least 99.99% and no gaps.Fourier analysisStudies the approximations and decomposition of functions using trigonometric polynomials.Format (file)（格式）Different programs require that information be specified to them in a formal manner, using particular keywords and ordering. This specification is a file format. Forward-backward algorithmUsed to train a hidden Markov model by aligning the model with training sequences. The algorithm then refines the model to reduce the error when fitted to the given data using a gradient descent approach.FTP (File Transfer Protocol)（文件传输协议）Allows a person to transfer files from one computer to another across a network using an FTP-capable client program. The FTP client program can only communicate with machines that run an FTP server. The server, in turn, will make a specific portion of its tile system available for FTP access, providing that the client is able to supply a recognized user name and password to the server.Full shotgun clone （鸟枪法克隆）A large-insert clone for which full shotgun sequence has been produced. Functional genomics（功能基因组学）Assessment of the function of genes identified by between-genome comparisons. The function of a newly identified gene is tested by introducing mutations into the gene and then examining the resultant mutant organism for an altered phenotype.gap （空位/间隙/缺口）A space introduced into an alignment to compensate for insertions and deletions in one sequence relative to another. To prevent the accumulation of too many gaps in an alignment, introduction of a gap causes the deduction of a fixed amount (the gap score) from the alignment score. Extension of the gap to encompass additional nucleotides or amino acid is also penalized in the scoring of an alignment. Gap penalty（空位罚分）A numeric score used in sequence alignment programs to penalize the presence of gaps within an alignment. The value of a gap penalty affects how often gaps appear in alignments produced by the algorithm. Most alignment programs suggest gap penalties that are appropriate for particular scoring matrices.Genetic algorithm（遗传算法）A kind of search algorithm that was inspired by the principles of evolution. A population of initial solutions is encoded and the algorithm searches through these by applying a pre-defined fitness measurement to each solution, selecting those with the highest fitness for reproduction. New solutions can be generated during this phase by crossover and mutation operations, defined in the encoded solutions. Genetic map （遗传图谱）A genome map in which polymorphic loci are positioned relative to one another on the basis of the frequency with which they recombine during meiosis. The unit of distance is centimorgans (cM), denoting a 1% chance of recombination.Genome（基因组）The genetic material of an organism, contained in one haploid set of chromosomes. Gibbs sampling methodAn algorithm for finding conserved patterns within a set of related sequences. A guessed alignment of all but one sequence is made and used to generate a scoring matrix that represents the alignment. The matrix is then matched to the left-out sequence, and a probable location of the corresponding pattern is found. This prediction is then input into a new alignment and another scoring matrix is produced and tested on a new left-out sequence. The process is repeated until there is no further improvement in the matrix.Global alignment（整体联配）Attempts to match as many characters as possible, from end to end, in a set of twomoresequences.Gopher (一个文档发布系统，允许检索和显示文本文件)Graph theory（图论）A branch of mathematics which deals with problems that involve a graph or network structure. A graph is defined by a set of nodes (or points) and a set of arcs (lines or edges) joining the nodes. In sequence and genome analysis, graph theory is used for sequence alignments and clustering alike genes.GSS（基因综述序列）Genome survey sequence.GUI（图形用户界面）Graphical user interface.H （相对熵值）H is the relative entropy of the target and background residue frequencies. (Karlin and Altschul, 1990). H can be thought of as a measure of the average information (in bits) available per position that distinguishes an alignment from chance. At high value s of H, short alignments can be distinguished by chance, whereas at lower H value s, a longer alignment may be necessary. (Altschul, 1991)Half-bitsSome scoring matrices are in half-bit units. These units are logarithms to the base 2 of odds scores times 2.Heuristic（启发式方法）A procedure that progresses along empirical lines by using rules of thumb to reach a solution. The solution is not guaranteed to be optimal.Hexadecimal system（16制系统）The base 16 counting system that uses the digits O-9 followed by the letters A-F. HGMP （人类基因组图谱计划）Human Genome Mapping Project.Hidden Markov Model (HMM)（隐马尔可夫模型）In sequence analysis, a HMM is usually a probabilistic model of a multiple sequence alignment, but can also be a model of periodic patterns in a single sequence, representing, for example, patterns found in the exons of a gene. In a model of multiple sequence alignments, each column of symbols in the alignment is represented by a frequency distribution of the symbols called a state, and insertions and deletions by other states. One then moves through the model along a particular path from state to state trying to match a given sequence. The next matching symbol is chosen from each state, recording its probability (frequency) and also the probability of going to that particular state from a previous one (the transition probability). State and transition probabilities are then multiplied to obtain a probability of the given sequence. Generally speaking, a HMM is a statistical model for an ordered sequence of symbols, acting as a stochastic state machine that generates a symbol each time a transition is made from one state to the next. Transitions betweenstates are specified by transition probabilities.Hidden layer（隐藏层）An inner layer within a neural network that receives its input and sends its outputto other layers within the network. One function of the hidden layer is to detect covariation within the input data, such as patterns of amino acid covariation that are associated with a particular type of secondary structure in proteins. Hierarchical clustering（分级聚类）The clustering or grouping of objects based on some single criterion of similarity or difference.An example is the clustering of genes in a microarray experiment based on the correlation between their expression patterns. The distance method used in phylogenetic analysis is another example.Hill climbingA nonoptimal search algorithm that selects the singular best possible solution at a given state or step. The solution may result in a locally best solution that is not a globally best solution.Homology（同源性）A similar component in two organisms (e.g., genes with strongly similar sequences) that can be attributed to a common ancestor of the two organisms during evolution. Horizontal transfer（水平转移）The transfer of genetic material between two distinct species that do not ordinarily exchange genetic material. The transferred DNA becomes established in the recipient genome and can be detected by a novel phylogenetic history and codon content com-pared to the rest of the genome.HSP （高比值片段对）High-scoring segment pair. Local alignments with no gaps that achieve one of the top alignment scores in a given search.HTGS/HGT（高通量基因组序列）High-throughout genome sequencesHTML（超文本标识语言）The Hyper-Text Markup Language (HTML) provides a structural description of a document using a specified tag set. HTML currently serves as the Internet lingua franca for describing hypertext Web page documents.HyperplaneA generalization of the two-dimensional plane to N dimensions.HypercubeA generalization of the three-dimensional cube to N dimensions.Identity （相同性/相同率）The extent to which two (nucleotide or amino acid) sequences are invariant. Indel（插入或删除的缩略语）An insertion or deletion in a sequence alignment.Information content (of a scoring matrix)A representation of the degree of sequence conservation in a column of ascoring matrix representing an alignment of related sequences. It is also the number of questions that must be asked to match the column to a position in a test sequence. For bases, the max-imum possible number is 2, and for proteins, 4.32 (logarithm to the base 2 of the number of possible sequence characters).Information theory（信息理论）。
生物信息学主要英文术语及释义
生物信息学主要英文术语及释义Coding region of DNA. See CDS.Expressed Sequence Tag (EST) （表达序列标签）Randomly selected, partial cDNA sequence; represents it's corresponding mRNA. dbEST is a large database of ESTs at GenBank, NCBI.FASTA （一种主要数据库搜索程序）The first widely used algorithm for database similarity searching. The program looks for optimal local alignments by scanning the sequence for small matches called "words". Initially, the scores of segments in which there are multiple word hits are calculated ("init1"). Later the scores of several segments may be summed to generate an "initn" score. An optimized alignment that includes gaps is shown in the output as "opt". The sensitivity and speed of the search are inversely related and controlled by the "k-tup" variable which specifies the size of a "word". (Pearson and Lipman)Extreme value distribution（极值分布）Some measurements are found to follow a distribution that has a long tail which decays at high value s much more slowly than that found in a normal distribution. This slow-falling type is called the extreme value distribution. The alignment scores between unrelated or random sequences are an example. These scores can reach very high value s, particularly when a large number of comparisons are made, as in a database similarity search. The probability of a particular score may be accurately predicted by the extreme value distribution, which follows a double negative exponential function after Gumbel.False negative（假阴性）A negative data point collected in a data set that was incorrectly reported due to a failure of the test in avoiding negative results.False positive （假阳性）A positive data point collected in a data set that was incorrectly reported due to a failure of the test. If the test had correctly measured the data point, the data would have been recorded as negative.Feed-forward neural network （反向传输神经网络）Organizes nodes into sequence layers in which the nodes in each layer are fully connected with the nodes in the next layer, except for the final output layer. Input is fed from the input layer through the layers in sequence in a “feed-forward” direction, resulting in output at the final layer. See also Neural network.Filtering (window size)During pair-wise sequence alignment using the dot matrix method, random matches can be filtered out by using a sliding window to compare the two sequences. Rather than comparing a single sequence position at a time, a window of adjacent positions in the two sequences is compared and a dot, indicating a match, is generated only if a certain minimal number of matches occur.Filtering （过滤）Also known as Masking. The process of hiding regions of (nucleic acid or amino acid) sequence having characteristics that frequently lead to spurious high scores. See SEG and DUST.Finished sequence（完成序列）Complete sequence of a clone or genome, with an accuracy of at least 99.99% and no gaps.Fourier analysisStudies the approximations and decomposition of functions using trigonometric polynomials.Format (file)（格式）Different programs require that information be specified to them in a formal manner, using particular keywords and ordering. This specification is a file format.Forward-backward algorithmUsed to train a hidden Markov model by aligning the model with training sequences. The algorithm then refines the model to reduce the error when fitted to the given data using a gradient descent approach.FTP (File Transfer Protocol)（文件传输协议）Allows a person to transfer files from one computer to another across a network using an FTP-capable client program. The FTP client program can only communicate with machines that run an FTP server. The server, in turn, will make a specific portion of its tile system available for FTP access, providing that the client is able to supply a recognized user name and password to the server.Full shotgun clone （鸟枪法克隆）A large-insert clone for which full shotgun sequence has been produced.Functional genomics（功能基因组学）Assessment of the function of genes identified by between-genome comparisons. The function of a newly identified gene is tested by introducing mutations into the gene and then examining the resultant mutant organism for an altered phenotype.gap （空位/间隙/缺口）A space introduced into an alignment to compensate for insertions and deletions in one sequence relative to another. To prevent the accumulation of too many gaps in an alignment, introduction of a gap causes the deduction of a fixed amount (the gap score) from the alignment score. Extension of the gap to encompass additional nucleotides or amino acid is also penalized in the scoring of an alignment. Gap penalty（空位罚分）A numeric score used in sequence alignment programs to penalize the presence of gaps within an alignment. The value of a gap penalty affects how often gaps appear in alignments produced by the algorithm. Most alignment programs suggest gap penalties that are appropriate for particular scoring matrices.Genetic algorithm（遗传算法）A kind of search algorithm that was inspired by the principles of evolution. A population of initial solutions is encoded and the algorithm searches through these by applying a pre-defined fitness measurement to each solution, selecting those with the highest fitness for reproduction. New solutions can be generated during this phase by crossover and mutation operations, defined in the encoded solutions.Genetic map （遗传图谱）A genome map in which polymorphic loci are positioned relative to one another on the basis of the frequency with which they recombine during meiosis. The unit of distance is centimorgans (cM), denoting a 1% chance of recombination.Genome（基因组）The genetic material of an organism, contained in one haploid set of chromosomes.Gibbs sampling methodAn algorithm for finding conserved patterns within a set of related sequences. A guessed alignment of all but one sequence is made and used to generate a scoring matrix that represents the alignment. The matrix is then matched to the left-out sequence, and a probable location of the corresponding pattern is found. This prediction is then input into a new alignment and another scoring matrix is produced and tested on a new left-out sequence. The process is repeated until there is no further improvement in the matrix.Global alignment（整体联配）Attempts to match as many characters as possible, from end to end, in a set of twomore sequences. Gopher (一个文档发布系统，允许检索和显示文本文件)Graph theory（图论）A branch of mathematics which deals with problems that involve a graph or network structure. A graph is defined by a set of nodes (or points) and a set of arcs (lines or edges) joining the nodes. In sequence and genome analysis, graph theory is used for sequence alignments and clustering alike genes.GSS（基因综述序列）Genome survey sequence.GUI（图形用户界面）Graphical user interface.H （相对熵值）H is the relative entropy of the target and background residue frequencies. (Karlin and Altschul, 1990).H can be thought of as a measure of the average information (in bits) available per position that distinguishes an alignment from chance. At high value s of H, short alignments can be distinguished by chance, whereas at lower H value s, a longer alignment may be necessary. (Altschul, 1991)Half-bitsSome scoring matrices are in half-bit units. These units are logarithms to the base 2 of odds scores times 2.Heuristic（启发式方法）A procedure that progresses along empirical lines by using rules of thumb to reach a solution. The solution is not guaranteed to be optimal.Hexadecimal system（16制系统）The base 16 counting system that uses the digits O-9 followed by the letters A-F.HGMP （人类基因组图谱计划）Human Genome Mapping Project.Hidden Markov Model (HMM)（隐马尔可夫模型）In sequence analysis, a HMM is usually a probabilistic model of a multiple sequence alignment, but can also be a model of periodic patterns in a single sequence, representing, for example, patterns found in the exons of a gene. In a model of multiple sequence alignments, each column of symbols in the alignment is represented by a frequency distribution of the symbols called a state, and insertions and deletions by other states. One then moves through the model along a particular path from state to state trying to match a given sequence. The next matching symbol is chosen from each state, recording its probability (frequency) and also the probability of going to that particular state from a previous one (the transition probability). State and transition probabilities are then multiplied to obtain a probability of the given sequence. Generally speaking, a HMM is a statistical model for an ordered sequence of symbols, acting as a stochastic state machine that generates a symbol each time a transition is made from one state to the next. Transitions betweenstates are specified by transition probabilities.Hidden layer（隐藏层）An inner layer within a neural network that receives its input and sends its output to other layers within the network. One function of the hidden layer is to detect covariation within the input data, such as patterns of amino acid covariation that are associated with a particular type of secondary structure in proteins.Hierarchical clustering（分级聚类）The clustering or grouping of objects based on some single criterion of similarity or difference.Anexample is the clustering of genes in a microarray experiment based on the correlation between their expression patterns. The distance method used in phylogenetic analysis is another example.Hill climbingA nonoptimal search algorithm that selects the singular best possible solution at a given state or step. The solution may result in a locally best solution that is not a globally best solution.Homology（同源性）A similar component in two organisms (e.g., genes with strongly similar sequences) that can be attributed to a common ancestor of the two organisms during evolution.Horizontal transfer（水平转移）The transfer of genetic material between two distinct species that do not ordinarily exchange genetic material. The transferred DNA becomes established in the recipient genome and can be detected by a novel phylogenetic history and codon content com-pared to the rest of the genome.HSP （高比值片段对）High-scoring segment pair. Local alignments with no gaps that achieve one of the top alignment scores in a given search.HTGS/HGT（高通量基因组序列）High-throughout genome sequencesHTML（超文本标识语言）The Hyper-Text Markup Language (HTML) provides a structural description of a document using a specified tag set. HTML currently serves as the Internet lingua franca for describing hypertext Web page documents.HyperplaneA generalization of the two-dimensional plane to N dimensions.HypercubeA generalization of the three-dimensional cube to N dimensions.Identity （相同性/相同率）The extent to which two (nucleotide or amino acid) sequences are invariant.Indel（插入或删除的缩略语）An insertion or deletion in a sequence alignment.Information content (of a scoring matrix)A representation of the degree of sequence conservation in a column of ascoring matrix representing an alignment of related sequences. It is also the number of questions that must be asked to match the column to a position in a test sequence. For bases, the max-imum possible number is 2, and for proteins, 4.32 (logarithm to the base 2 of the number of possible sequence characters).Information theory（信息理论）A branch of mathematics that measures information in terms of bits, the minimal amount of structural complexity needed to encode a given piece of information.Input layer（输入层）The initial layer in a feed-forward neural net. This layer encodes input information that will be fed through the network model.Interface definition languageUsed to define an interface to an object model in a programming language neutral form, where an interface is an abstraction of a service defined only by the operations that can be performed on it. Internet（因特网）The network infrastructure, consisting of cables interconnected by routers, that pro-vides global connectivity for individual computers and private networks of computers. A second sense of the word internet is the collective computer resources available over this global network.Interpolated Markov modelA type of Markov model of sequences that examines sequences for patterns of variable length in order to discriminate best between genes and non-gene sequences.Intranet（内部网）Intron （内含子）Non-coding region of DNA.Iterative（反复的/迭代的）A sequence of operations in a procedure that is performed repeatedly.Java（一种由SUN Microsystem开发的编程语言）K （BLAST程序的一个统计参数）A statistical parameter used in calculating BLAST scores that can be thought of as a natural scale for search space size. The value K is used in converting a raw score (S) to a bit score (S').K-tuple（字/字长）Identical short stretches of sequences, also called words.lambda （λ，BLAST程序的一个统计参数）A statistical parameter used in calculating BLAST scores that can be thought of as a natural scale for scoring system. The value lambda is used in converting a raw score (S) to a bit score (S').LAN（局域网）Local area network.Likelihood（似然性）The hypothetical probability that an event which has already occurred would yield a specific outcome. Unlike probability, which refers to future events, likelihood refers to past events. Linear discriminant analysisAn analysis in which a straight line is located on a graph between two sets of data pointsin a location that best separates the data points into two groups.Local alignment（局部联配）Attempts to align regions of sequences with the highest density of matches. In doing so, one or more islands of subalignments are created in the aligned sequences.Log odds score（概率对数值）The logarithm of an odds score. See also Odds score.Low Complexity Region (LCR) （低复杂性区段）Regions of biased composition including homopolymeric runs, short-period repeats, and more subtle overrepresentation of one or a few residues. The SEG program is used to mask or filter LCRs in amino acid queries. The DUST program is used to mask or filter LCRs in nucleic acid queries.Machine learning（机器学习）The training of a computational model of a process or classification scheme to distinguish between alternative possibilities.Markov chain（马尔可夫链）Describes a process that can be in one of a number of states at any given time. The Markov chain is defined by probabilities for each transition occurring; that is, probabilities of the occurrence of state sj given that the current state is sp Substitutions in nucleic acid and protein sequences are generally assumed to follow a Markov chain in that each site changes independently of the previous history ofthe site. With this model, the number and types of substitutions observed over a relatively short period of evolutionary time can be extrapolated to longer periods of time. In performing sequence alignments and calculating the statistical significance of alignment scores, sequences are assumed to be Markov chains in which the choice of one sequence position is not influenced by another.Masking （过滤）Also known as Filtering. The removal of repeated or low complexity regions from a sequence in order to improve the sensitivity of sequence similarity searches performed with that sequence.Maximum likelihood (phylogeny, alignment)（最大似然法）The most likely outcome (tree or alignment), given a probabilistic model of evolutionary change in DNA sequences.Maximum parsimony（最大简约法）The minimum number of evolutionary steps required to generate the observed variation in a set of sequences, as found by comparison of the number of steps in all possible phylogenetic trees.Method of momentsThe mean or expected value of a variable is the first moment of the value s of the variable around the mean, defined as that number from which the sum of deviations to all value s is zero. The standard deviation is the second moment of the value s about the mean, and so on.Minimum spanning treeGiven a set of related objects classified by some similarity or difference score, the mini-mum spanning tree joins the most-alike objects on adjacent outer branches of a tree and then sequentially joins less-alike objects by more inward branches. The tree branch lengths are calculated by the same neighbor-joining algorithm that is used to build phylogenetic trees of sequences from a distance matrix. The sum of the resulting branch lengths between each pair of objects will be approximately that found by the classification scheme.MMDB （分子建模数据库）Molecular Modelling Database. A taxonomy assigned database of PDB (see PDB) files, and related information.Molecular clock hypothesis（分子钟假设）The hypothesis that sequences change at the same rate in the branches of an evolutionarytree.Monte Carlo（蒙特卡罗法）A method that samples possible solutions to a complex problem as a way to estimate a more general solution.Motif （模序）A short conserved region in a protein sequence. Motifs are frequently highly conserved parts of domains.Multiple Sequence Alignment （多序列联配）An alignment of three or more sequences with gaps inserted in the sequences such that residues with common structural positions and/or ancestral residues are aligned in the same column. Clustal W is one of the most widely used multiple sequence alignment programsMutation data matrix（突变数据矩阵，即PAM矩阵）A scoring matrix compiled from the observation of point mutations between aligned sequences. Also refers to a Dayhoff PAM matrix in which the scores are given as log odds scores.N50 length （N50长度，即覆盖50%所有核苷酸的最大序列重叠群长度）A measure of the contig length (or scaffold length) containing a 'typical' nucleotide. Specifically, it isthe maximum length L such that 50% of all nucleotides lie in contigs (or scaffolds) of size at least L. Nats (natural logarithm)A number expressed in units of the natural logarithm.NCBI （美国国家生物技术信息中心）National Center for Biotechnology Information (USA). Created by the United States Congress in 1988, to develop information systems to support thebiological research community.Needleman-Wunsch algorithm（Needleman-Wunsch算法）Uses dynamic programming to find global alignments between sequences.Neighbor-joining method（邻接法）Clusters together alike pairs within a group of related objects (e.g., genes with similar sequences) to create a tree whose branches reflect the degrees of difference among the objects.Neural network（神经网络）From artificial intelligence algorithms, techniques that involve a set of many simple units that hold symbolic data, which are interconnected by a network of links associated with numeric weights. Units operate only on their symbolic data and on the inputs that they receive through their connections. Most neural networks use a training algorithm (see Back-propagation) to adjust connection weights, allowing the network to learn associations between various input and output patterns. See also Feed-forward neural network.NIH （美国国家卫生研究院）National Institutes of Health (USA).Noise（噪音）In sequence analysis, a small amount of randomly generated variation in sequences that is added to a model of the sequences; e.g., a hidden Markov model or scoring matrix, in order to avoid the model overfitting the sequences. See also Overfitting.Normal distribution（正态分布）The distribution found for many types of data such as body weight, size, and exam scores. The distribution is a bell-shaped curve that is described by a mean and standard deviation of the mean. Local sequence alignment scores between unrelated or random sequences do not follow this distribution but instead the extreme value distribution which has a much extended tail for higher scores. See also Extreme value distribution.Object Management Group (OMG)（国际对象管理协作组）A not-for-profit corporation that was formed to promote component-based software by introducing standardized object software. The OMG establishes industry guidelines and detailed object management specifications in order to provide a common framework for application development. Within OMG is a Life Sciences Research group, a consortium representing pharmaceutical companies, academic institutions, software vendors, and hardware vendors who are working together to improve communication and inter-operability among computational resources in life sciences research. See CORBA.Object-oriented database（面向对象数据库）Unlike relational databases (see entry), which use a tabular structure, object-oriented databases attempt to model the structure of a given data set as closely as possible. In doing so, object-oriented databases tend to reduce the appearance of duplicated data and the complexity of query structure often found in relational databases.Odds score（概率/几率值）The ratio of the likelihoods of two events or outcomes. In sequence alignments and scoring matrices,the odds score for matching two sequence characters is the ratio of the frequency with which the characters are aligned in related sequences divided by the frequency with which those same two characters align by chance alone, given the frequency of occurrence of each in the sequences. Odds scores for a set of individually aligned positions are obtained by multiplying the odds scores for each position. Odds scores are often converted to logarithms to create log odds scores that can be added to obtain the log odds score of a sequence alignment.OMIM （一种人类遗传疾病数据库）Online Mendelian Inheritance in Man. Database of genetic diseases with references to molecular medicine, cell biology, biochemistry and clinical details of the diseases.Optimal alignment（最佳联配）The highest-scoring alignment found by an algorithm capable of producing multiple solutions. This is the best possible alignment that can be found, given any parameters supplied by the user to the sequence alignment program.ORF （开放阅读框）Open Reading Frame. A series of codons (base triplets) which can be translated into a protein. There are six potential reading frames of an unidentifed sequence; TBLASTN (see BLAST) transalates a nucleotide sequence in all six reading frames, into a protein, then attempts to align the results to sequeneces in a protein database, returning the results as a nucleotide sequence. The most likely reading frame can be identified using on-line software (e.g. ORF Finder).Orthologous（直系同源）Homologous sequences in different species that arose from a common ancestral gene during speciation; may or may not be responsible for a similar function. A pair of genes found in two species are orthologous when the encoded proteins are 60-80% identical in an alignment. The proteins almost certainly have the same three-dimensional structure, domain structure, and biological function, and the encoding genes have originated from a common ancestor gene at an earlier evolutionary time. Two orthologs 1 and II in genomes A and B, respectively, may be identified when the complete genomes of two species are available: (1) in a database similarity search of all of the proteome of B using I as a query, II is the best hit found, and (2) I is the best hit when 11 is used as a query of the proteome of B. The best hit is the database sequence with the highest expect value (E). Orthology is also predicted by a very close phylogenetic relationship between sequences or by a cluster analysis. Compare to Paralogs. See also Cluster analysis.Output layer（输出层）The final layer of a neural network in which signals from lower levels in the network are input into output states where they are weighted and summed togive an outpu t signal. For example, the output signal might be the prediction of one type of protein secondary structure for the central amino acid in a sequence window.OverfittingCan occur when using a learning algorithm to train a model such as a neural net or hid-den Markov model. Overfitting refers to the model becoming too highly representative of the training data and thus no longer representative of the overall range of data that is supposed to be modeled.。
基因工程外文翻译（中英对照）（可编辑）
基因工程外文翻译(中英对照)Retrovirus-mediated gene transfer and expression cloning: Powerful tools in functional genomics Most of the human genome has now been sequenced and about 30,000 potential open reading frames have been identified, indicating that we use these 30,000 genes to functionally organize our biologic activities. However, functions of many genes are still unknown despite intensive efforts using bioinformatics as well as transgenic and knockout mice. Retrovirus-mediated gene transfer is a powerful tool that can be used to understand gene functions. We have developed a variety of retrovirus vectors and efficient packaging cell lines that have facilitated the development of efficient functional expression cloning methods. In this review, we describe retrovirus-mediated strategies used for investigation of gene functions and function-based screening strategies 2003 International Society for Experimental Hematology. Published by Elsevier Inc.摘要:人类基因组的大部分现在已经测序完成,大约30,000潜在的开放阅读框已经确定,表明我们使用这30,000个基因管理我们的生物学活和功能性。
生物信息学和基因数据分析
生物信息学和基因数据分析一、生物信息学基本概念1.生物信息学的定义：生物信息学是一门交叉学科，它利用计算机技术、数学方法、统计学原理等手段，对生物学信息进行采集、存储、分析、整合和解释，以揭示生物体的生物学规律。
2.生物信息学的研究内容：基因组学、蛋白质组学、代谢组学、转录组学等。
3.生物信息学的方法和技术：计算机编程、数据库构建、数据分析、机器学习、人工智能等。
二、基因数据分析1.基因数据分析的定义：基因数据分析是对基因组序列信息进行挖掘和解读，以揭示基因的结构、功能及其在生物过程中的作用。
2.基因数据分析的方法：a)序列比对：将待研究的基因序列与已知的基因序列进行比较，以确定其同源性。
b)结构预测：利用生物信息学方法预测基因的三维结构。
c)功能注释：对基因的功能进行预测和注释，如编码蛋白质的功能、调控元件的功能等。
d)表达分析：研究基因在特定生物过程中的表达水平，以及表达模式的变化。
e)调控网络分析：构建基因间的调控关系网络，以揭示生物体的生物学过程。
3.基因数据分析的工具和软件：a)BLAST：序列比对工具。
b)Clustal Omega：序列比对和结构分析工具。
c)Geneious：生物信息学综合分析平台。
d)Cufflinks：RNA-seq数据分析和基因表达量计算工具。
e)GEO、ArrayExpress：公共基因表达数据仓库。
4.基因数据分析在生物科学研究中的应用：a)疾病基因挖掘：发现与疾病相关的基因，为疾病诊断和治疗提供依据。
b)功能基因研究：揭示基因在生物过程中的功能，为生物技术研发提供理论基础。
c)进化研究：分析基因在不同物种中的演化规律，揭示生物进化的机制。
三、生物信息学和基因数据分析的发展趋势1.人工智能在生物信息学中的应用：利用深度学习、自然语言处理等技术，提高生物信息学分析的准确性和效率。
2.大数据在基因数据分析中的应用：整合多源数据，挖掘基因表达、调控、结构等方面的规律。
生物信息学
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（二）基因组时代的生物信息学
以基因组计划的实施为标志的基因组时代（1990年至2001年） 是生物信息学成为一个较完整的新兴学科并得到高速发 展的时期。这一时期生物信息学确立了自身的研究领域 和学科特征，成为生命科学的热点学科和重要前沿领域 之一。 这一阶段的主要成就包括大分子序列以及表达序列标签 （expressed sequence tag，EST）数据库的高速发展、 BLAST（basic local alignment search tool）和FASTA （fast alignment）等工具软件的研制和相应新算法的提 出、基因的寻找与识别、电子克隆（in silico cloning）技 术等，大大提高了管理和利用海量数据的能力。
16 U. Wash (Hood LAB) 14,15
人类基因组计划准备用15年时 间投入30亿美元，完成人全部 24(22+X+Y)条染色体中3.2×109个 碱基对的序列测定，主要任务包 括做图（遗传图谱＼物理图谱以 及转录图谱的绘制）、测序和基 因识别，其根本任务是解读和破 译生物体的生老病死以及与疾病 相关的遗传信息。
Non-coding DNA 约60% 约40% 分散重复序列
假基因
基因片段
内含子
串联重复序列/ 成簇重复序列
估计10万→最初公布3.5万→目前研究确定2.45万
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结构基因组学时期
生物信息学的研究
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主要的数据库资源
核酸序列数据库主要有GenBank, EMBL, DDBJ等. 蛋白质序列数据库主要有SWISS-PROT, PIR, TrEMBL等，
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我国对人类基因组计划的贡献
No Center Region 1,6,9,10,13,20,22,X (Clones from Wash U) 2,3,4,7,11,15,18,Y 5,16,19 1,2,3,X 21,18,11q 8,21,X Most of 14 3p 10 17,21,X 21, reg of 9 8 2,6,8,22,21 Total 900 250 230 160 50 85 30 50 6.9 6 23 30 2671 2671Mb 11 27 4663Kr 2950Kr 75 Size(Mb) 850 6/1-8/31/99 Actual K 1300 837 865 687 462 136 180 100 12.5 5 40 12 Projected Kr Proj Accum. Genbank Kr 4/1-11/30/99 Mr. 4/99-3/00 941 296 559 461 261 195 32 118 12.5 4200 2900 2300 2100 660 520 180 300 >100 150 40 50 137 110 40 13687Kr >12 8 7.9 6.4 3.1 2.1 1.5 1.4 0.5 0.45 0.3 0.3 0.29 0.23 0.17 32.64Mr 1 Sanger Centre 2 WIBR 3 Wash U 4 JGI 5 Baylor 6 Riken 7 IMB 8 Genoscope 9 U. Wash (Olson) 10 Beijing 11 GTC (Smith) 12 MPIMG 13 GBF 14 Stanford (Davis) 15 Keio
生物信息学名词解释
行者【转载】生物信息学名词解释----这个比较全什么是高通量测序？高通量测序技术（High-throughput sequencing，HTS）是对传统Sanger测序（称为一代测序技术）革命性的改变, 一次对几十万到几百万条核酸分子进行序列测定, 因此在有些文献中称其为下一代测序技术(next generation sequencing，NGS )足见其划时代的改变, 同时高通量测序使得对一个物种的转录组和基因组进行细致全貌的分析成为可能, 所以又被称为深度测序(Deep sequencing)。
什么是Sanger法测序（一代测序）Sanger法测序利用一种DNA聚合酶来延伸结合在待定序列模板上的引物。
直到掺入一种链终止核苷酸为止。
每一次序列测定由一套四个单独的反应构成，每个反应含有所有四种脱氧核苷酸三磷酸(dNTP)，并混入限量的一种不同的双脱氧核苷三磷酸(ddNTP)。
由于ddNTP缺乏延伸所需要的3-OH基团，使延长的寡聚核苷酸选择性地在G、A、T或C处终止。
终止点由反应中相应的双脱氧而定。
每一种dNTPs和ddNTPs的相对浓度可以调整，使反应得到一组长几百至几千碱基的链终止产物。
它们具有共同的起始点，但终止在不同的的核苷酸上，可通过高分辨率变性凝胶电泳分离大小不同的片段，凝胶处理后可用X-光胶片放射自显影或非同位素标记进行检测。
什么是基因组重测序（Genome Re-sequencing）全基因组重测序是对基因组序列已知的个体进行基因组测序，并在个体或群体水平上进行差异性分析的方法。
随着基因组测序成本的不断降低，人类疾病的致病突变研究由外显子区域扩大到全基因组范围。
通过构建不同长度的插入片段文库和短序列、双末端测序相结合的策略进行高通量测序，实现在全基因组水平上检测疾病关联的常见、低频、甚至是罕见的突变位点，以及结构变异等，具有重大的科研和产业价值。
什么是de novo测序de novo测序也称为从头测序：其不需要任何现有的序列资料就可以对某个物种进行测序，利用生物信息学分析手段对序列进行拼接，组装，从而获得该物种的基因组图谱。
生物信息学A卷答案
一、名词辨析（每题5分，共20分）1、基因与基因组：Gene 基因：遗传功能的单位。
它是一种DNA序列，在有些病毒中则是一种RNA 序列，它编码功能性蛋白质或RNA分子。
Genome 基因组：染色体组，一个生物体、细胞器或病毒的整套基因；例如，细胞核基因组，叶绿体基因组，噬菌体基因组。
2、相似性与同源性：所谓同源序列，简单地说，是指从某一共同祖先经趋异进化而形成的不同序列。
同源性可以用来描述染色体—“同源染色体”、基因—“同源基因”和基因组的一个片断—“同源片断”必须指出，相似性(similarity)和同源性(homology)是两个完全不同的概念。
相似性是指序列比对过程中用来描述检测序列和目标序列之间相同DNA碱基或氨基酸残基顺序所占比例的高低。
相似性本身的含义，并不要求与进化起源是否同一、与亲缘关系的远近、甚至于结构与功能有什么联系。
3、CDS与cDNA：cDNA序列：互补DNA序列，指的是mRNA为在逆转录酶的作用下将形成DNA 的过程。
CDS序列：编码序列,从起始密码子到终止密码子的所有序列。
4、数据库搜索和数据库查询：数据库查询：对序列、结构以及各种二次数据库中的注释信息进行关键词匹配查找（又称数据库检索）。
数据库搜索：通过特定的序列相似性比对算法，找出核酸或蛋白质序列数据库中与检测序列具有一定程度相似性的序列。
搜索对象不是数据库的注释信息，而是序列信息。
二、判断题（20分）1、生物信息学可以理解为生命科学中的信息科学。
（√）2、DNA分子和蛋白质分子都含有进化信息。
（√）3、目前生命科学研究的重点和突破点的已完全转移到生物信息学上，已不需要实验做支撑。
（×）4、生物信息学的发展大致经历了三个阶段：前基因组时代、基因组时代和后基因组时代。
（√）5、基因组与蛋白质组一样，都处于动态变化之中。
（×）6、蛋白质三维结构都是静态的，在行使功能的过程中其结构不会改变。
（×）7、生物信息学中研究的生物大分子主要是脂类和多糖。
基因组和生物信息学相关名词
一、真核基因组相关名词解释基因家族（gene family ）：真核细胞中许多相关的基因常按功能成套组合，称为基因家族。
同一家族中的成员有时紧密排列在一起，称为一个基因簇；有时分散在同一染色体不同的部位，甚至分散在不同的染色体上。
基因簇（gene cluster）：基因家族各成员聚集成簇。
假基因（pseudogene）：与功能基因序列相似，却没有功能。
超基因家族（gene superfamily ）：序列不同但功能相似的一组基因。
断裂基因：DNA分子中基因编码序列常被非编码的序列隔开，这类基因称为断裂基因。
编码序列称为外显子（exon）；非编码序列称为内含子（intron）。
剪接：内含子从原初转录本中除去的加工过程称为剪接，包括内含子从原初转录本中删除以及外显子末端的共价连结。
在成熟的RNA中出现的序列称为外显子。
在原初转录本加工时被删除的插入序列称为内含子。
二、HGP相关名词解释遗传图谱：又称连锁图，是指基因或DNA标志在染色体上的相对位置与遗传距离。
遗传距离通常由基因或DNA片断在染色体交换过程中分离的频率厘摩（cM ）来表示。
1厘摩表示每次减数分裂的重组频率为１％。
厘摩值越高表明两点之间距离越远，厘摩值越低表示两点间距离越近。
用于遗传图谱绘制的常用遗传标记为RFLP、STR、SNP。
RFLP：restriction fragment length polymorphism，限制性酶切片段长度多态性，DNA序列的变化引起限制性内切酶位点丢失或产生，从而导致酶切片段长度的变化。
SNP：single nucleotide polymorphism，单核苷酸的多态性，指单个核苷酸的变化而从产生的多态性。
物理图谱：指以已知核苷酸序列的DNA片段（如STS）为路标，以碱基对作为基本测量单位的两点之间的实际距离。
通常由DNA的限制酶片段或克隆的DNA片段有序排列而成。
STS：sequence tagged site，序列标签位点，是指染色体定位明确，并且可用PCR扩增的单拷贝短DNA序列。
生物信息分析常用名词解释
生物信息分析常用名词解释生物信息学（bioinformatics）：综合计算机科学、信息技术和数学的理论和方法来研究生物信息的交叉学科。
包括生物学数据的研究、存档、显示、处理和模拟，基因遗传和物理图谱的处理，核苷酸和氨基酸序列分析，新基因的发现和蛋白质结构的预测等。
基因组（genome)：是指一个物种的单倍体的染色体数目，又称染色体组。
它包含了该物种自身的所有基因。
基因（gene）：是遗传信息的物理和功能单位，包含产生一条多肽链或功能RNA所必需的全部核苷酸序列。
基因组学：（genomics)是指对所有基因进行基因组作图（包括遗传图谱、物理图谱、转录图谱）、核酸序列测定、基因定位和基因功能分析的科学。
基因组学包括结构基因组学（structural genomics)、功能基因组学（functional genomics)、比较基因组学(Comparative genomics)宏基因组学：宏基因组是基因组学一个新兴的科学研究方向。
宏基因组学（又称元基因组学，环境基因组学，生态基因组学等），是研究直接从环境样本中提取的基因组遗传物质的学科。
传统的微生物研究依赖于实验室培养，元基因组的兴起填补了无法在传统实验室中培养的微生物研究的空白。
蛋白质组学（proteomics）：阐明生物体各种生物基因组在细胞中表达的全部蛋白质的表达模式及功能模式的学科。
包括鉴定蛋白质的表达、存在方式(修饰形式)、结构、功能和相互作用等。
遗传图谱：指通过遗传重组所得到的基因线性排列图。
物理图谱：是利用限制性内切酶将染色体切成片段，再根据重叠序列把片段连接称染色体，确定遗传标记之间的物理距离的图谱。
转录图谱：是利用EST作为标记所构建的分子遗传图谱。
基因文库：用重组DNA技术将某种生物细胞的总DNA 或染色体DNA的所有片断随机地连接到基因载体上,然后转移到适当的宿主细胞中，通过细胞增殖而构成各个片段的无性繁殖系（克隆），在制备的克隆数目多到可以把某种生物的全部基因都包含在内的情况下，这一组克隆的总体就被称为某种生物的基因文库。
生物信息学重点
名词解释：1、基因组：生物有机体的单倍体细胞中所有DNA,包括核中的染色体DNA和线粒体、叶绿体等亚细胞器中的DNA。
2、蛋白质组：指一个基因组所表达的全部蛋白质。
3、信号肽：新合成多肽链中用于指导蛋白质的跨膜转移（定位）的N-末端的氨基酸序列（有时不一定在N端）。
4、启动子：一段特定的直接与RNA聚合酶及其转录因子相结合，决定基因转录起始与否的DNA序列。
同源序列一般是相似的，相似序列不一定是同源的5、引物：（primer）指一段较短的单链RNA或DNA，它能与DNA的一条链配对提供游离的3’-OH末端以作为DNA聚合酶合成脱氧核苷酸链的起始点。
6、直向同源、垂直同源：（Orthologous ）描述在不同物种中来自于共同祖先的基因。
Orthologous基因可能有相同的功能，也可能没有。
7、GenBank：是美国国家生物技术信息中心管理的核酸序列数据库，汇集并注释了所有公开的核酸序列。
8、ORF：一组连续的含有三联密码子的能够被翻译成为多肽链的DNA序列。
它由起始密码子开始，到终止密码子结束。
9、CDS：是编码一段蛋白产物的序列。
10、BLAST：是一个基于局部比对的序列相似性搜索工具。
11、EST：（表达序列标签）就是cDNA的一个片段，即一个基因编码序列的一小段。
12、PDB：（蛋白质结构数据库）是美国国家实验室创建并管理的收录生物大分子晶体结构的数据库。
13、Homology：（同源性）14、Similarity：（相似性）15、Orthologous：（直向同源、垂直同源）描述在不同物种中来自于共同祖先的基因。
Orthologous基因可能有相同的功能，也可能没有。
16、Entrez：是NCBI网站的数据库查询系统，它集成了文献数据库、核酸序列数据库、结构数据库、基因图谱数据库，是有效利用NCBI数据库资源的工具。
17、EMBL：是欧洲分子生物学实验室创建的核酸序列数据库。
18、DDBJ：日本国立遗传研究所创建的核酸序列数据库。
生物信息学bioinformatics(近完整版) Microsoft Word 文档 (2)1
一．什么是生物信息学？Genome informatics is a scientific discipline that encompasses all aspects of genome information acquisition, processing, storage, distribution, analysis, and interpretation. （它是一个学科领域，包含着基因组信息的获取、处理、存储、分配、分析和解释的所有方面。
）(The U.S. Human Genome Project: The First Five Y ears FY 1991-1995, by NIH and DOE)生物信息学是把基因组DNA序列信息分析作为源头，破译隐藏在DNA序列中的遗传语言，特别是非编码区的实质；同时在发现了新基因信息之后进行蛋白质空间结构模拟和预测。
生物信息学的研究目标是揭示“基因组信息结构的复杂性及遗传语言的根本规律”。
它是本世纪自然科学和技术科学领域中“基因组、“信息结构”和“复杂性”这三个重大科学问题的有机结合。
How to find the coding regions in rude DNA sequence?By signals or By contentsAmong the types of functional sites in genomic DNA that researchers have sought to recognize are splice sites, start and stop codons, branch points, promoters and terminators of transcription, polyadenylation sites, ribosomal binding sites, topoisomerase II binding sites, topoisomerase I cleavage sites, and various transcription factor binding sites. Local sites such as these are called signals and methods for detecting them may be called signal sensors.二．新基因和新SNPs的发现与鉴定大部分新基因是靠理论方法预测出来的。
生物信息学主要英文术语及释义（续完）
⽣物信息学主要英⽂术语及释义（续完）These substitutions may be found in an amino acid substitution matrix such as the Dayhoff PAM and Henikoff BLOSUM matrices. Columns in the alignment that include gaps are not scored in the calculation. Perceptron（感知器，模拟⼈类视神经控制系统的图形识别机) A neural network in which input and output states are directly connected without intervening hidden layers. PHRED （⼀种⼴泛应⽤的原始序列分析程序，可以对序列的各个碱基进⾏识别和质量评价） A widely used computer program that analyses raw sequence to produce a 'base call' with an associated 'quality score' for each position in the sequence. A PHRED quality score of X corresponds to an error probability of approximately 10-X/10. Thus, a PHRED quality score of30 corresponds to 99.9% accuracy for the base call in the raw read. PHRAP （⼀种⼴泛应⽤的原始序列组装程序） A widely used computer program that assembles raw sequence into sequence contigs and assigns to each position in the sequence an associated 'quality score', on the basis of the PHRED scores of the raw sequence reads. A PHRAP quality score of X corresponds to an error probability of approximately 10-X/10. Thus, a PHRAP quality score of 30 corresponds to 99.9% accuracy for a base in the assembled sequence. Phylogenetic studies（系统发育研究） PIR （主要蛋⽩质序列数据库之⼀，翻译⾃GenBank） A database of translated GenBank nucleotide sequences. PIR is a redundant (see Redundancy) protein sequence database. The database is divided into four categories: PIR1 - Classified and annotated. PIR2 - Annotated. PIR3 -Unverified. PIR4 - Unencoded or untranslated. Poisson distribution（帕松分布） Used to predict the occurrence of infrequent events over a long period of time 143or when there are a large number of trials. In sequence analysis, it is used to calculate the chance that one pair of a large number of pairs of unrelated sequences may give a high local alignment score. Position-specific scoring matrix (PSSM)（特定位点记分矩阵，PSI-BLAST等搜索程序使⽤） The PSSM gives the log-odds score for finding a particular matching amino acid in a target sequence. Represents the variation found in the columns of an alignment of a set of related sequences. Each subsequent matrix column corresponds to the next column in the alignment and each row corresponds to a particular sequence character (one of four bases in DNA sequences or 20 amino acids in protein sequences). Matrix values are log odds scores obtained by dividing the counts of the residue in the alignment, dividing by the expected number of counts based on sequence composition, and converting the ratio to a log score. The matrix is moved along sequences to find similar regions by adding the matching log odds scores and looking for high values. There is no allowance for gaps. Also called a weight matrix or scoring matrix. Posterior (Bayesian analysis) A conditional probability based on prior knowledge and newly uated relationships among variables using Bayes rule. See also Bayes rule. Prior (Bayesian analysis) The expected distribution of a variable based on previous data. Profile（分布型） A matrix representation of a conserved region in a multiple sequence alignment that allows for gaps in the alignment. The rows include scores for matching sequential columns of the alignment to a test sequence. The columns include substitution scores for amino acids and gap penalties. See also PSSM. Profile hidden Markov model（分布型隐马尔可夫模型） A hidden Markov model of a conserved region in a multiple sequence alignment that includes gaps and may be used to search new sequences for similarity to the aligned sequences. Proteome（蛋⽩质组） The entire collection of proteins that are encoded by the genome of an organism. Initially the proteome is estimated by gene prediction and annotation methods but eventually will be revised as more information on the sequence of the expressed genes is obtained. Proteomics （蛋⽩质组学） Systematic analysis of protein expression_r of normal and diseased tissues that involves the separation, identification and characterization of all of the proteins in an organism. Pseudocounts Small number of counts that is added to the columns of a scoring matrix to increase the variability either to avoid zero counts or to add more variation than was found in the sequences used to produce the matrix. 144PSI-BLAST （BLAST系列程序之⼀） Position-Specific Iterative BLAST. An iterative search using the BLAST algorithm. A profile is built after the initial search, which is then used in subsequent searches. The process may be repeated, if desired with new sequences found in each cycle used to refine the profile. Details can be found in this discussion of PSI-BLAST. (Altschul et al.) PSSM （特定位点记分矩阵） See position-specific scoring matrix and profile. Public sequence databases （公共序列数据库，指GenBank、EMBL和DDBJ） The three coordinated international sequence databases: GenBank, the EMBL data library and DDBJ. Q20 (Quality score 20) A quality score of > or = 20 indicates that there is less than a 1 in 100 chance that the base call is incorrect. These are consequently high-quality bases. Specifically, the quality value "q" assigned to a basecall is defined as: q = -10 x log10(p) where p is the estimated error probability for that basecall. Note that high quality values correspond to low error probabilities, and conversely. Quality trimming This is an algorithm which uses a sliding window of 50 bases and trims from the 5' end of the read followed by the 3' end. With each window, the number of low quality (10 or less) bases is determined. If more than 5 bases are below the threshold quality, the window is incremented by one base and the process is repeated. When the low quality test fails, the position where it stopped is recorded. The parameters for window length low quality threshold and number of low quality bases tolerated are fixed. The positions of the 5' and 3' boundaries of the quality region are noted in the plot of quality values presented in the" Chromatogram Details" report. Query （待查序列/搜索序列） The input sequence (or other type of search term) with which all of the entries in a database are to be compared. Radiation hybrid (RH) map （辐射杂交图谱） A genome map in which STSs are positioned relative to one another on the basis of the frequency with which they are separated by radiation-induced breaks. The frequency is assayed by analysing a panel of human–hamster hybrid cell lines, each produced by lethally irradiating human cells and fusing them with recipient hamster cells such that each carries a collection of human chromosomal fragments. The unit of distance is centirays (cR), denoting a 1% chanceof a break occuring between two loci Raw Score （初值，指最初得到的联配值S） The score of an alignment, S, calculated as the sum of substitution and gap scores. Substitution scores are given by a look-up table (see PAM, BLOSUM). Gap scores are typically calculated as the sum of G, the gap opening penalty 145and L, the gap extension penalty. For a gap of length n, the gap cost would be G+Ln. The choice of gap costs, G and L is empirical, but it is customary to choose a high value for G (10-15)and a low value for L (1-2). Raw sequence （原始序列/读胶序列） Individual unassembled sequence reads, produced by sequencing of clones containing DNA inserts. Receiver operator characteristic The receiver operator characteristic (ROC) curve describes the probability that a test will correctly declare the condition present against the probability that the test will declare the condition present when actually absent. This is shown through a graph of the tesls sensitivity against one minus the test specificity for different possible threshold values. Redundancy （冗余） The presence of more than one identical item represents redundancy. In bioinformatics, the term is used with reference to the sequences in a sequence database. If a database is described as being redundant, more than one identical (redundant) sequence may be found. If the database is said to be non-redundant (nr), the database managers have attempted to reduce the redundancy. The term is ambiguous with reference to genetics, and as such, the degree of non-redundancy varies according to the database manager's interpretation of the term. One can argue whether or not two alleles of a locus defines the limit of redundancy, or whether the same locus in different, closely related organisms constitutes redundency. Non-redundant databases are, in some ways, superior, but are less complete. These factors should be taken into consideration when selecting a database to search. Regular expression_rs This computational tool provides a method for expressing the variations found in a set of related sequences including a range of choices at one position, insertions, repeats, and so on. For example, these expression_rs are used to characterize variations found in protein domains in the PROSITE catalog. Regularization A set of techniques for reducing data overfitting when training a model. See also Overfitting. Relational database（关系数据库）Organizes information into tables where each column represents the fields of informa-tion that can be stored in a single record. Each row in the table corresponds to a single record. A single database can have many tables and a query language is used to access the data. See also Object-oriented database. Scaffold （⽀架，由序列重叠群拼接⽽成） The result of connecting contigs by linking information from paired-end reads from plasmids, paired-end reads from BACs, known messenger RNAs or other sources. The contigs in a scaffold are ordered and oriented with respect to one another. 146 Scoring matrix（记分矩阵） See Position-specific scoring matrix. SEG （⼀种蛋⽩质程序低复杂性区段过滤程序） A program for filtering low complexity regions in amino acid sequences. Residues that have been masked are represented as "X" in an alignment. SEG filtering is performed by default in the blastp subroutine of BLAST 2.0. (Wootton and Federhen) Selectivity (in database similarity searches)（数据库相似性搜索的选择准确性） The ability of a search method to locate members of a protein family without making a false-positive classification of members of other families. Sensitivity (in database similarity searches)（数据库相似性搜索的灵敏性） The ability of a search method to locate as many members of a protein family as possi-ble, including distant members of limited sequence similarity. Sequence Tagged Site （序列标签位点） Short cDNA sequences of regions that have been physically mapped. STSs provide unique landmarks, or identifiers, throughout the genome. Useful as a framework for further sequencing. Significance（显著⽔平） A significant result is one that has not simply occurred by chance, and therefore is prob-ably true. Significance levels show how likely a result is due to chance, expressed as a probability. In sequence analysis, the significance of an alignment score may be calcu-lated as the chance that such a score would be found between random or unrelated sequences. See Expect value. Similarity score (sequence alignment) （相似性值） Similarity means the extent to which nucleotide or protein sequences are related. The extent of similarity between two sequences can be based on percent sequence identity and/or conservation. In BLAST similarity refers to a positive matrix score. The sum of the number of identical matches and conservative (high scoring) substitu-tions in a sequence alignment divided by the total number of aligned sequence charac-ters. Gaps are usually ignored. Simulated annealing A search algorithm that attempts to solve the problem of finding global extrema. The algorithm was inspired by the physical cooling process of metals and the freezing process in liquids where atoms slow down in movement and line up to form a crystal. The algorithm traverses the energy levels of a function, always accepting energy levels that are smaller than previous ones, but sometimes accepting energy levels that are greater, according to the Boltzmann probability distribution. Single-linkage cluster analysis An analysis of a group of related objects, e.g., similar proteins in different genomes to identify both close and more distant relationships, represented on a tree or dendogram. The method joins the most closely related pairs by the neighbor-joining algorithm by representing these pairs as outer branches on 147the tree. More distant objects are then pro-gressively added to lower tree branches. The method is also used to predict phylogenet-ic relationships by distance methods. See also Hierarchical clustering, Neighbor-joining method. Smith-Waterman algorithm（Smith-Waterman算法） Uses dynamic programming to find local alignments between sequences. The key fea-ture is that all negative scores calculated in the dynamic programming matrix are changed to zero in order to avoid extending poorly scoring alignments and to assist in identifying local alignments starting and stopping anywhere with the matrix. SNP （单核苷酸多态性） Single nucleotide polymorphism, or a single nucleotide position in the genome sequence for which two or more alternative alleles are present at appreciable frequency (traditionally, at least 1%) in the human population. Space or time complexity（时间或空间复杂性） An algorithms complexity is the maximum amount of computer memory or time required for the number of algorithmic steps to solve a problem. Specificity (in database similarity searches)（数据库相似性搜索的特异性） The ability of a search method to locate members of one protein family, including dis-tantly related members. SSR （简单序列重复） Simple sequence repeat, a sequence consisting largely of a tandem repeat of a specific k-mer (such as (CA)15). Many SSRs are polymorphic and have been widely used in genetic mapping. Stochastic context-free grammar A formal representation of groups of symbols in different parts of a sequence; i.e., not in the same context. An example is complementary regions in RNA that will form sec-ondary structures. The stochastic feature introduces variability into such regions. Stringency Refers to the minimum number of matches required within a window. See also Filtering. STS （序列标签位点的缩写） See Sequence Tagged Site Substitution （替换） The presence of a non-identical amino acid at a given position in an alignment. If the aligned residues have similar physico-chemical properties the substitution is said to be "conservative". Substitution Matrix （替换矩阵） A substitution matrix containing values proportional to the probability that amino acid i mutates into amino acid j for all pairs of amino acids. such matrices are constructed by assembling a large and diverse sample of verified pairwise alignments of amino acids. If the sample is large enough to be statistically significant, the resulting matrices should reflect the true probabilities of mutations occuring through a period of evolution. 148Sum of pairs method Sums the substitution scores of all possible pair-wise combinations of sequence charac-ters in one column of a multiple sequence alignment. SWISS-PROT （主要蛋⽩质序列数据库之⼀） A non-redundant (See Redundancy) protein sequence database. Thoroughly annotated and cross referenced. A subdivision is TrEMBL. Synteny The presence of a set of homologous genes in the same order on two genomes. Threading In protein structure prediction, the aligning of the sequence of a protein of unknown structure with a known three-dimensional structure to determine whether the amino acid sequence is spatially and chemically compatible with that structure. TrEMBL （蛋⽩质数据库之⼀，翻译⾃EMBL） A protein sequence database of Translated EMBL nucleotide sequences. Uncertainty（不确定性） From information theory, a logarithmic measure of the average number of choices that must be made for identification purposes. See also Information content. Unified Modeling Language (UML) A standard sanctioned by the Object Management Group that provides a formal nota-tion for describing object-oriented design. UniGene （⼈类基因数据库之⼀） Database of unique human genes, at NCBI. Entries are selected by near identical presence in GenBank and dbEST databases. The clusters of sequences produced are considered to represent a single gene. Unitary Matrix （⼀元矩阵） Also known as Identity Matrix.A scoring system in which only identical characters receive a positive score. URL（统⼀资源定位符） Uniform resource locator. Viterbi algorithm Calculates the optimal path of a sequence through a hidden Markov model of sequences using a dynamic programming algorithm. Weight matrix See Position-specifc scoring matrix.。
生信 基础概念
生信基础概念1. 基因组学（Genomics）：基因组学是研究生物体基因组的学科。
它涉及基因组的测序、组装、注释和比较分析等方面，以了解基因组的结构、功能和进化。
2. 转录组学（Transcriptomics）：转录组学是研究生物体转录组的学科。
它关注转录本（mRNA）的表达水平、差异表达、剪接变体等，以揭示基因的转录调控和表达模式。
3. 蛋白质组学（Proteomics）：蛋白质组学是研究生物体蛋白质组的学科。
它包括蛋白质的鉴定、定量、修饰和相互作用等方面，以了解蛋白质的功能、结构和代谢途径。
4. 数据挖掘（Data Mining）：数据挖掘是从大量数据中提取有用信息和模式的过程。
在生物信息学中，数据挖掘技术用于发现生物数据中的隐藏规律、相关性和模式。
5. 序列比对（Sequence Alignment）：序列比对是将两个或多个生物分子的序列进行比较的过程。
它用于识别相似性、同源性和进化关系。
6. 生物信息学数据库（Bioinformatics Databases）：生物信息学数据库是存储和管理生物数据的资源。
这些数据库包括基因组序列、蛋白质序列、基因表达数据等，可以用于数据查询、分析和下载。
7. 生物信息学工具（Bioinformatics Tools）：生物信息学工具是用于处理和分析生物数据的软件和程序。
这些工具包括序列比对工具、基因注释工具、数据可视化工具等。
8. 系统生物学（Systems Biology）：系统生物学是将生物体系视为一个整体，研究生物分子之间的相互作用和网络关系的学科。
它涉及到基因、蛋白质、代谢物等多个层次的分析。
以上是生物信息学的一些基础概念，生物信息学在基因组学、转录组学、蛋白质组学等领域有着广泛的应用，为生物研究提供了强大的分析和计算工具。
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Big Genomic Data in Bioinformatics CloudAbstractThe achievement of Human Genome project has led to the proliferation of genomic sequencing data. This along with the next generation sequencing has helped to reduce the cost of sequencing, which has further increased the demand of analysis of this large genomic data. This data set and its processing has aided medical researches.Thus, we require expertise to deal with biological big data. The concept of cloud computing and big data technologies such as the Apache Hadoop project, are hereby needed to store, handle and analyse this data. Because, these technologies provide distributed and parallelized data processing and are efficient to analyse even petabyte (PB) scale data sets. However, there are some demerits too which may include need of larger time to transfer data and lesser network bandwidth, majorly.人类基因组计划的实现导致基因组测序数据的增殖。
这与下一代测序一起有助于降低测序的成本，这进一步增加了对这种大基因组数据的分析的需求。
该数据集及其处理有助于医学研究。
因此，我们需要专门知识来处理生物大数据。
因此，需要云计算和大数据技术（例如Apache Hadoop项目）的概念来存储，处理和分析这些数据。
因为，这些技术提供分布式和并行化的数据处理，并且能够有效地分析甚至PB级的数据集。
然而，也有一些缺点，可能包括需要更大的时间来传输数据和更小的网络带宽，主要。
IntroductionThe introduction of next generation sequencing has given unrivalled levels of sequence data. So, the modern biology is incurring challenges in the field of data management and analysis.A single human's DNA comprises around 3 billion base pairs (bp) representing approximately 100 gigabytes (GB) of data. Bioinformatics is encountering difficulty in storage and analysis of such data. Moore's Law infers that computers double in speed and half in size every 18 months. And reports say that the biological data will accumulate at even faster pace [1]. Sequencing a human genome has decreased in cost from $1 million in 2007 to $1 thousand in 2012. With this falling cost of sequencing and after the completion of the Human Genome project in 2003, inundate of biological sequence data was generated. Sequencing and cataloguing genetic information has increased many folds (as can be observed from the GenBank database of NCBI). Various medical research institutes like the National Cancer Institute are continuously targeting on sequencing of a million genomes for the understanding of biological pathways and genomic variations to predict the cause of the disease. Given, the whole genome of a tumour and a matching normal tissue sample consumes 0.1 TB of compressed data, then one million genomes will require 0.1 million TB, i.e. 103 PB (petabyte) [2]. The explosion of Biology's data (the scale of the data exceeds a single machine) has made it more expensive to store, process and analyse compared to its generation. This has stimulated the use of cloud to avoid large capital infrastructure and maintenance costs.In fact, it needs deviation from the common structured data (row-column organisation) to a semi-structured or unstructured data. And there is a need to develop applications that execute in parallel on distributed data sets. With the effective use of big data in the healthcare sector, areduction of around 8% in expenditure is possible, that would account for $300 billion saving annually.下一代测序的引入给出了无与伦比的序列数据水平。
因此，现代生物学在数据管理和分析领域面临挑战。
单个人类DNA包含约30亿个碱基对（bp），表示约100吉字节（GB）的数据。
生物信息学在这种数据的存储和分析中遇到困难。
摩尔定律推测，计算机速度增加了一倍，每18个月大小减少一半。
报告说，生物数据将以更快的速度积累[1]。
人类基因组测序的成本从2007年的100万美元降至2012年的1千美元。
随着测序成本的下降，在2003年人类基因组项目完成后，产生了生物序列数据的淹没。
测序和编目遗传信息已经增加了许多倍（如从NCBI的GenBank数据库可以观察到的）。
诸如国家癌症研究所的各种医学研究机构正在连续地将一百万个基因组的测序用于理解生物学途径和基因组变异以预测疾病的原因。
假定肿瘤的全基因组和匹配的正常组织样品消耗0.1 TB的压缩数据，则一百万基因组将需要10万TB，即103 PB（petabyte）[2]。
生物学数据的爆炸（数据的规模超过单个机器）使得与其一代相比存储，处理和分析更昂贵。
这刺激了云的使用，以避免大的资本基础设施和维护成本。
实际上，它需要从公共结构化数据（行- 列组织）偏移到半结构化或非结构化数据。
并且需要开发在分布式数据集上并行执行的应用程序。
随着医疗行业大数据的有效利用，支出减少约8％，每年可节省3000亿美元。
ReviewCloud computingCloud computing is defined as "a pay-per-use model for enabling convenient, on-demand network access to a shared pool of configurable computing resources (e.g., networks, servers, storage, applications and services) that can be rapidly provisioned and released with minimal management effort or service provider interaction" [3]. Some of the major concepts involved are grid computing, distributed systems, parallelised programming and visualization technology. A single physical machine can host multiple virtual machines through virtualisation technology. Problem with grid computing was that effort was majorly spent on maintaining the robustness and resilience of the cluster itself. Big data technologies now have identified solutions to process huge parallelised data sets cost effectively. Cloud computing and big data technologies are two different things, one is facilitating the cost effective storage and the other is a Platform as a Service (PaaS), respectively。