Open AccessFinding Protein and Nucleotide Similarities with FASTA
Author(s) -
Pearson William R.
Publication year - 2016
Publication title -
current protocols in bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.535
H-Index - 57
eISSN - 1934-340X
pISSN - 1934-3396
DOI - 10.1002/0471250953.bi0309s53
Subject(s) - similarity (geometry) , computer science , set (abstract data type) , sequence alignment , computational biology , nearest neighbor search , variety (cybernetics) , range (aeronautics) , data mining , biology , genetics , artificial intelligence , programming language , peptide sequence , engineering , gene , image (mathematics) , aerospace engineering
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. 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. 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. © 2016 by John Wiley & Sons, Inc.