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2016 ; 53
(ä): 3.9.1-3.9.25
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Finding Protein and Nucleotide Similarities with FASTA
#MMPMID27010337
Pearson WR
Curr Protoc Bioinformatics
2016[Mar]; 53
(ä): 3.9.1-3.9.25
PMID27010337
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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.
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