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Bioinformatics. 2007 May 1;23(9):1073-9. Epub 2007 Mar 1.

COBALT: constraint-based alignment tool for multiple protein sequences.

Author information

  • 1National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA.

Abstract

MOTIVATION:

A tool that simultaneously aligns multiple protein sequences, automatically utilizes information about protein domains, and has a good compromise between speed and accuracy will have practical advantages over current tools.

RESULTS:

We describe COBALT, a constraint based alignment tool that implements a general framework for multiple alignment of protein sequences. COBALT finds a collection of pairwise constraints derived from database searches, sequence similarity and user input, combines these pairwise constraints, and then incorporates them into a progressive multiple alignment. We show that using constraints derived from the conserved domain database (CDD) and PROSITE protein-motif database improves COBALT's alignment quality. We also show that COBALT has reasonable runtime performance and alignment accuracy comparable to or exceeding that of other tools for a broad range of problems.

AVAILABILITY:

COBALT is included in the NCBI C++ toolkit. A Linux executable for COBALT, and CDD and PROSITE data used is available at: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt

PMID:
17332019
[PubMed - indexed for MEDLINE]
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