Computing multiple sequence/structure alignments with the T-coffee package

TitleComputing multiple sequence/structure alignments with the T-coffee package
Publication TypeJournal Article
Year of Publication2004
AuthorsNotredame C, Suhre K
JournalCurr Protoc Bioinformatics
VolumeChapter 3
PaginationUnit3 8
Date PublishedFeb
Accession Number18428722
KeywordsAlgorithms, Programming Languages, Sequence Alignment/ methods, Sequence Analysis/ methods, Software
Abstract

The FASTA package provides a comprehensive set of similarity searching programs, similar to those provided by the BLAST package, and some additional programs for searching with short peptides and oligonucleotides that are not provided by BLAST. The FASTA programs work with a wide variety of database formats, including mySQL sequence databases. FASTA provides very accurate statistical significance estimates, and is more sensitive than BLASTN when comparing DNA sequences. These protocols describe how to use the FASTA programs to characterize protein and DNA sequences, using protein:protein, protein:DNA, and DNA:DNA comparisons.