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Bioinformatics Advance Access published online on February 10, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl046
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 8, 2005
Revised December 20, 2005
Accepted February 6, 2006

Article

Development and validation of a consistency based multiple structure alignment algorithm

Jessica Ebert 1 and Douglas Brutlag 1 *

1 Program in Biophysics and Department of Biochemistry, Stanford University, Stanford, CA 94305 USA


  Abstract

Summary: We introduce an algorithm that uses the information gained from simultaneous consideration of an entire group of related proteins to create multiple structure alignments. CBA (consistency-based alignment) first harnesses the information contained within regions that are consistently aligned among a set of pairwise superpositions in order to realign pairs of proteins through both global and local refinement methods. It then constructs a multiple alignment that is maximally consistent with the improved pairwise alignments. We validate CBA's alignments by assessing their accuracy in regions where at least two of the aligned structures contain the same conserved sequence motif.

Results: CBA correctly aligns well over 90% of motif residues in superpositions of proteins belonging to the same family or superfamily, and outperforms a number of previously reported multiple structure alignment algorithms.

Availability: CBA is available at http://cba.stanford.edu/, and source code is freely available at http://brutlag.stanford.edu/software/.

Associate Editor: Thomas Lengauer
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