生物信息学课件_L5

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Formatting options
可以对比对结果的显示格式、显示内容进行调整
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Explanation of Blast Result
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Filter 的不同显示形式
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Distance tree of results
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Multiple alignment
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ቤተ መጻሕፍቲ ባይዱ
Multiple alignment Parameters
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View the E value (statistical evaluation), Bit Scores
(identities and conservation) , check the “query coverage” if necessary
Local Extreme matrics and Total Matrics
Do the proteins (query and subject) share a common motif or


signature? Are the proteins part of a reasonable multiple sequence alignment? Do the proteins share a similar biological function? Do the proteins share a similar three-dimensional structure? Use the doubtful marginal match result (maybe a distantly related protein) as a query to perform a new BLAST search, check the result.
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搜索结果过多情况
加Entrez限制条件, 如对数据库的限定, 对搜索序列的物

搜索结果过少情况

种或序列长度的限定等 利用序列的一部分进行搜索 调整记分矩阵 调整期望值
去掉Entrez限制 提高期望值 使用更高PAM值或更低BLOSUM值的记分矩阵 高级BLAST搜索
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与 Basic BLAST中的 nucleotide blast或protein blast 使用相同的查询序 列输入界面
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问题：进行序列 的对库相似性分 析还有其他方法/ 程序吗？
/Tools/sss/
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There are exons (protein-coding sequences) and introns (intervening sequences) in the genomic DNA , and there may be sequencing errors or polymorphisms
Sometimes we want the comparison between chromosome
sequences of closely/distantly related species, In any comparison, genomic changes may have occurred.
Sometimes we want to know the small differences between DNA
sequences, e.g. SNPs
Blast-related tools are designed to address these needs.
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Recently developed tools include:

How to perform alignment? Different algorithms
Types of alignment (Global vs. Local, pairwise vs. multiple) Dynamic Programming
▪ Needleman-Wunsch (global sequence alignment) ▪ Smith-Waterman (local sequence alignment) ▪ BLAST (heuristic versions of Smith-Waterman)
SSAHA at Ensembl uses a similar strategy as BLAT.
See
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For blastn, the default word size is 11. Changing word size is like changing threshold of involved sequences. w=15 gives fewer matches and is faster than w=11 or w=7. For megablast, the default word size is 28 and can be adjusted to 64 or more. What will this do? Megablast is VERY fast for finding closely related DNA sequences!
high similar sequences)

MEGABLAST is a powerful tool for gene predictions, analyzing single-nucleotide polymorphisms, and some other tasks.
Result assessment (E value, bit score, identities/positives +
coverage)
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The problem of assigning homology between genes or proteins is not solved by sequence analysis alone: it is also necessary to apply biological criteria to support the inference of homology, such as, the evaluations of protein structures and function.
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Optimized for aligning very long and/or highly-similar sequences (>95% identity) Search targets include
Entire eukaryotic genomes (of the same or closely related
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BLAST search with PAEP as a query finds many other lipocalins
This is the evidence that PAEP and lipocalin are homologous.

Recall (召回) of the recent blast result: Request ID, valid in 24h.
Blast程序的类型 (blastn, blastp, blastx, tblastn, tblastx) Searching steps (choose program, input data, parameter
options such as databases, word size, matrix, E cutoff.., output formatting options)
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高级BLAST及多序列比对
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Advanced BLAST
MegaBLAST PSI-BLAST PHI-BLAST

Multiple Sequence Alignment
Definition Properties, features and uses Scoring MSA Mainly methods to get MSA ▪ Progressive: ClustalW, T-COFFEE
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Sometimes a real match is hard to infer by standard blast…
Using NP_006735 as query sequence, blastp in nr database, and the outputs are restricted to homo sapiens (organism)
MegaBLAST at NCBI.
BLAT (BLAST-like alignment tool).
BLAT parses an entire genomic DNA database into words (11mers), then searches them against a query. Thus it is a mirror image of the BLAST strategy. See
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BLAST
定义: a database similarity searching tool, find the local
similarity regions between sequences, calculate the statistical significance of matches
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Output format (formatting options)
Graphic summary
Filter results

Other reports
Search summary, Taxonomy report, Distance tree of