Finding Protein and Nucleotide Similarities with FASTA.
Finding Protein and Nucleotide Similarities with FASTA.
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DOI：
10.1002/0471250953.bi0309s53
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发表时间：
2016-03-24
影响因子：
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通讯作者：
Pearson, William R
中科院分区：
文献类型：
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作者：
Pearson, William R
FASTA程序提供了一套全面的快速相似性搜索工具（fasta36、fastx36、tfastx36、fasty36、tfasty36），类似于BLAST软件包提供的工具，以及用于较慢、最佳、局部和全局相似性搜索的程序（ssearch36、ggsearch36）和用于短肽和寡核苷酸搜索的程序（fasts36、fastm36）。FASTA程序使用经验策略来估计统计显著性，该策略适应一系列相似性评分矩阵和空位罚分，提高比对边界准确性和搜索灵敏度（单元3.5）。FASTA程序可以产生“BLAST样”比对和表格输出，以便于整合到现有的分析管道中，并且可以搜索小的代表性数据库，然后使用来自较小数据集的链接报告较大序列集的结果。FASTA程序可以处理各种各样的数据库格式，包括mySQL和PostgreSQL数据库（第9.4单元）。这些程序还提供了一种将结构域和活性位点注释整合到比对中并突出功能关键残基的突变状态的策略。这些协议描述了如何使用FASTA程序来表征蛋白质和DNA序列，使用蛋白质：蛋白质，蛋白质：DNA和DNA：DNA比较。
The FASTA programs provide a comprehensive set of rapid similarity searching tools ( fasta36, fastx36, tfastx36, fasty36, tfasty36), similar to those provided by the BLAST package, as well as programs for slower, optimal, local and global similarity searches ( ssearch36, ggsearch36) and for searching with short peptides and oligonucleotides ( fasts36, fastm36). The FASTA programs use an empirical strategy for estimating statistical significance that accommodates a range of similarity scoring matrices and gap penalties, improving alignment boundary accuracy and search sensitivity (Unit 3.5). The FASTA programs can produce “BLAST-like” alignment and tabular output, for ease of integration into existing analysis pipelines, and can search small, representative databases, and then report results for a larger set of sequences, using links from the smaller dataset. The FASTA programs work with a wide variety of database formats, including mySQL and postgreSQL databases (Unit 9.4). The programs also provide a strategy for integrating domain and active site annotations into alignments and highlighting the mutational state of functionally critical residues. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons.