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Bioinformatics 2007 23(2):e24-e29; doi:10.1093/bioinformatics/btl311
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org

Biological Sequence Analysis

Multiple alignment by sequence annealing

Ariel S. Schwartz 1,* and Lior Pachter 2

1 EECS, Computer Science Division, University of California Berkeley, CA 94720, USA
2 Department of Mathematics, University of California Berkeley, CA 94720, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: We introduce a novel approach to multiple alignment that is based on an algorithm for rapidly checking whether single matches are consistent with a partial multiple alignment. This leads to a sequence annealing algorithm, which is an incremental method for building multiple sequence alignments one match at a time. Our approach improves significantly on the standard progressive alignment approach to multiple alignment.

Results: The sequence annealing algorithm performs well on benchmark test sets of protein sequences. It is not only sensitive, but also specific, drastically reducing the number of incorrectly aligned residues in comparison to other programs. The method allows for adjustment of the sensitivity/specificity tradeoff and can be used to reliably identify homologous regions among protein sequences.

Availability: An implementation of the sequence annealing algorithm is available at http://bio.math.berkeley.edu/amap/

Contact: sariel{at}cs.berkeley.edu


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