UNIT 3.8 Computing Multiple Sequence/Structure Alignments with the T-Coffee Package

  1. Cedric Notredame1,2,
  2. Karsten Suhre2

Published Online: 1 FEB 2004

DOI: 10.1002/0471250953.bi0308s04

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Notredame, C. and Suhre, K. 2004. Computing Multiple Sequence/Structure Alignments with the T-Coffee Package. Current Protocols in Bioinformatics. 4:3.8:3.8.1–3.8.28.

Author Information

  1. 1

    Swiss Institute of Bioinformatics, Epalinges, Switzerland

  2. 2

    Information Genetique et Structurale, CNRS, Marseilles, France

Publication History

  1. Published Online: 1 FEB 2004
  2. Published Print: DEC 2003

This is not the most recent version of the article. View current version (1 MAR 2010)


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.