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Bioinformatics Advance Access published online on October 20, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti719
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received August 10, 2005
Revised September 28, 2005
Accepted October 14, 2005

Applications note

ConFind: a robust tool for conserved sequence identification

James A. Smagala 1, Erica D. Dawson 1, Martin Mehlmann 1, Michael B. Townsend 1, Robert D. Kuchta 1, and Kathy L. Rowlen 1*

1 Department of Chemistry and Biochemistry, The University of Colorado at Boulder, UCB #215, Boulder, CO, 80309, USA

* To whom correspondence should be addressed.
Kathy L. Rowlen, E-mail: rowlen{at}colorado.edu


  Abstract

Summary: ConFind (CONserved region FINDer) identifies regions of conservation in multiple sequence alignments that can serve as diagnostic targets. Designed to work with a large number of closely related, highly variable sequences, ConFind provides robust handling of alignments containing partial sequences and ambiguous characters. Conserved regions are defined in terms of minimum region length, maximum informational entropy (variability) per position, number of exceptions allowed to the maximum entropy criterion, and the minimum number of sequences that must contain a non-ambiguous character at a position to be considered for inclusion in a conserved region. Comparison of the calculated entropy for an alignment of 95 influenza A hemagglutinin sequences with random deletions results in a 98% reduction in the average error in ConFind relative to the ‘Find Conserved Regions’ option in BioEdit.

Requirements: ConFind requires Python 2.3, but Python 2.4 or an upgrade of the optparse module to Optik 1.5 is suggested. The program is known to run under Linux and DOS.

Availability: ConFind is licensed under the GNU General Public License (GPL). Source code, documentation, and a precompiled DOS executable are available for download at http://www.colorado.edu/chemistry/RGHP/software/.


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