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Bioinformatics Advance Access originally published online on March 1, 2007
Bioinformatics 2007 23(9):1073-1079; doi:10.1093/bioinformatics/btm076
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Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.


  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

Contact: richa{at}helix.nih.gov

Associate Editor: Charlie Hodgman

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

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