NCBI常见术语(缩略词)详解
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ASN.1
Abstract Syntax Notation 1 is an international standard data-representation format used to achieve interoperability between computer platforms. It allows for the reliable exchange of data in terms of structure and content by computer and software systems of all types.
build
A run of the genome assembly and annotation process of the set of products generated by that run.
CCAP
Cancer Chromosome Aberration APwas designed to expedite the definition and detailed characterization of the distinct chromosomal alterations that are associated with malignant transformation. The project is a collaboration among theNCI, theNCBI, and numerous research labs.
blastp
protein–proteinBLAST.blastptakes protein sequences inFASTAformat,GenBankAccession numbers, orGInumbers and compares them against theNCBIProtein databases.
API
Application Programming Interface. AnAPIis a set of routines that an application uses to request and carry out lower-level services performed by a computer's operating system. For computers running a graphical user interface, anAPImanages an application's windows, icons, menus, and dialog boxes.
BLAT
ADNA/Protein sequence analysis program to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments.BLATon proteins finds sequences of 80% and greater similarity of length 20 amino acids or more.BLATis notBLAST. (See theBLAT web page.)
BAC
Bacterial Artificial Chromosome. ABACis a large segment ofDNA(100,000–200,000 bp) from another species cloned into bacteria. Once the foreignDNAhas been cloned into the host bacteria, many copies of it can be made.
BLOB
Binary Large Object (or binary data object).BLOBrefers to a large piece of data, such as a bitmap. ABLOBis characterized by large field values, an unpredictable table size, and data that are formless from the perspective of a program. It is also a keyword designating theBLOBstructure, which contains information about a block of data.
cDNA
complementaryDNA. ADNAsequence obtained by reverse transcription of a messengerRNA(mRNA) sequ, coding sequence.CDSrefers to the portion of a genomicDNAsequence that is translated, from the startcodonto the stopcodon, inclusively, if complete. A partialCDSlacks part of the completeCDS(it may lack either or both the start and stopcodons). Successful translation of aCDSresults in the synthesis of a protein.
BLAST
Basic Local Alignment Search Tool (Altschul et al., J Mol Biol 215:403-410; 1990). A sequence comparisonalgorithmthat is optimized for speed and used to search sequence databases for optimal local alignments to a query. See theBLASTchapter (Chapter 15) or thetutorialor the narrativeguidetoBLAST.
bit score
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. By normalizing a raw score using the formula:
引用NCBI常见术语（缩略词）详解
3-D or 3D
Three-dimensional.
Accession number
AnAccession numberis a unique identifier given to a sequence when it is submitted to one of theDNArepositories (GenBank,EMBL,DDBJ). The initial deposition of a sequence record is referred to as version 1. If the sequence is updated, the version number is incremented, but theAccession numberwill remain constant.
a “bit score” S′ is attained, which has a standard set of units, and where K andlambdaare the statistical parameters of the scoring system. Becausebit scoreshave been normalized with respect to the scoring system, they can be used to compare alignment scores from different searches.
CDART
ConservedDomainArchitecture Retrieval Tool. When given a protein query sequence,CDARTdisplays the functionaldomainsthat make up the protein and lists proteins with similardomainarchitectures. The functionaldomainsfor a sequence are found by comparing the protein sequence to a database of conserveddomainalignments,CDDusingRPS-BLAST.
allele
One of the variant forms of a gene at a particularlocuson a chromosome. Differentallelesproduce variation in inherited characteristics such as hair color or blood type. In an individual, one form of theallele(the dominant one) may be expressed more than another form (the recessive one). When “genes” are considered simply as segments of a nucleotide sequence,allelerefers to each of the possible alternative nucleotides at a specific position in the sequence. For example, a CTpolymorphismsuch as CCT[C/T]CCAT would have twoalleles: C and T.
blastn
nucleotide–nucleotideBLAST.blastntakes nucleotide sequences inFASTAformat,GenBankAccession numbers, orGInumbers and compares them against theNCBINucleotide databases.
CDD
ConservedDomainDatabase. This database is a collection of sequence alignments and profiles representing proteindomainsconserved during molecular evolution.
CD
ConservedDomain.CDrefers to adomain(a distinct functional and/or structural unit of a protein) that has been conserved during evolution. During evolution, changes at specific positions of an amino acid sequence in the protein have occurred in a way that preserve the physico-chemical properties of the original residues, and hence the structural and/or functional properties of that region of the protein.
Abstract Syntax Notation 1 is an international standard data-representation format used to achieve interoperability between computer platforms. It allows for the reliable exchange of data in terms of structure and content by computer and software systems of all types.
build
A run of the genome assembly and annotation process of the set of products generated by that run.
CCAP
Cancer Chromosome Aberration APwas designed to expedite the definition and detailed characterization of the distinct chromosomal alterations that are associated with malignant transformation. The project is a collaboration among theNCI, theNCBI, and numerous research labs.
blastp
protein–proteinBLAST.blastptakes protein sequences inFASTAformat,GenBankAccession numbers, orGInumbers and compares them against theNCBIProtein databases.
API
Application Programming Interface. AnAPIis a set of routines that an application uses to request and carry out lower-level services performed by a computer's operating system. For computers running a graphical user interface, anAPImanages an application's windows, icons, menus, and dialog boxes.
BLAT
ADNA/Protein sequence analysis program to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments.BLATon proteins finds sequences of 80% and greater similarity of length 20 amino acids or more.BLATis notBLAST. (See theBLAT web page.)
BAC
Bacterial Artificial Chromosome. ABACis a large segment ofDNA(100,000–200,000 bp) from another species cloned into bacteria. Once the foreignDNAhas been cloned into the host bacteria, many copies of it can be made.
BLOB
Binary Large Object (or binary data object).BLOBrefers to a large piece of data, such as a bitmap. ABLOBis characterized by large field values, an unpredictable table size, and data that are formless from the perspective of a program. It is also a keyword designating theBLOBstructure, which contains information about a block of data.
cDNA
complementaryDNA. ADNAsequence obtained by reverse transcription of a messengerRNA(mRNA) sequ, coding sequence.CDSrefers to the portion of a genomicDNAsequence that is translated, from the startcodonto the stopcodon, inclusively, if complete. A partialCDSlacks part of the completeCDS(it may lack either or both the start and stopcodons). Successful translation of aCDSresults in the synthesis of a protein.
BLAST
Basic Local Alignment Search Tool (Altschul et al., J Mol Biol 215:403-410; 1990). A sequence comparisonalgorithmthat is optimized for speed and used to search sequence databases for optimal local alignments to a query. See theBLASTchapter (Chapter 15) or thetutorialor the narrativeguidetoBLAST.
bit score
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. By normalizing a raw score using the formula:
引用NCBI常见术语（缩略词）详解
3-D or 3D
Three-dimensional.
Accession number
AnAccession numberis a unique identifier given to a sequence when it is submitted to one of theDNArepositories (GenBank,EMBL,DDBJ). The initial deposition of a sequence record is referred to as version 1. If the sequence is updated, the version number is incremented, but theAccession numberwill remain constant.
a “bit score” S′ is attained, which has a standard set of units, and where K andlambdaare the statistical parameters of the scoring system. Becausebit scoreshave been normalized with respect to the scoring system, they can be used to compare alignment scores from different searches.
CDART
ConservedDomainArchitecture Retrieval Tool. When given a protein query sequence,CDARTdisplays the functionaldomainsthat make up the protein and lists proteins with similardomainarchitectures. The functionaldomainsfor a sequence are found by comparing the protein sequence to a database of conserveddomainalignments,CDDusingRPS-BLAST.
allele
One of the variant forms of a gene at a particularlocuson a chromosome. Differentallelesproduce variation in inherited characteristics such as hair color or blood type. In an individual, one form of theallele(the dominant one) may be expressed more than another form (the recessive one). When “genes” are considered simply as segments of a nucleotide sequence,allelerefers to each of the possible alternative nucleotides at a specific position in the sequence. For example, a CTpolymorphismsuch as CCT[C/T]CCAT would have twoalleles: C and T.
blastn
nucleotide–nucleotideBLAST.blastntakes nucleotide sequences inFASTAformat,GenBankAccession numbers, orGInumbers and compares them against theNCBINucleotide databases.
CDD
ConservedDomainDatabase. This database is a collection of sequence alignments and profiles representing proteindomainsconserved during molecular evolution.
CD
ConservedDomain.CDrefers to adomain(a distinct functional and/or structural unit of a protein) that has been conserved during evolution. During evolution, changes at specific positions of an amino acid sequence in the protein have occurred in a way that preserve the physico-chemical properties of the original residues, and hence the structural and/or functional properties of that region of the protein.