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Bioinformatics Advance Access published online on March 1, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm076
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COBALT: COnstraint Based ALignment Tool for Multiple Protein Sequences

Jason S. Papadopoulos and Richa Agarwala

National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bldg. 38A, Room 10-03N, 8600 Rockville Pike, Bethesda, MD 20894 USA

*To whom correspondence should be addressed. Dr. Richa Agarwala, E-mail: richa{at}helix.nih.gov


  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 software 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

Associate Editor: Charlie Hodgman

Received on September 15, 2006; revised on January 23, 2007; accepted on February 26, 2007

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