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Bioinformatics Advance Access published online on June 29, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl351
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received May 12, 2006
Revised June 21, 2006
Accepted June 23, 2006

Article

An iterative refinement algorithm for consistency based multiple structural alignment methods

Yu Chen 1 and Gordon M. Crippen 2 *

1 Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA
2 College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA

* To whom correspondence should be addressed.
Gordon M. Crippen, E-mail: gcrippen{at}umich.edu


  Abstract

Motivation: Multiple STructural Alignment (MSTA) provides valuable information for solving problems such as fold recognition. The consistency based approach tries to find conflict-free subsets of alignments from a pre-computed all-to-all Pairwise Alignment Library (PAL). If large proportions of conflicts exist in the library, consistency can be hard to get. On the other hand, multiple structural superposition has been used in many MSTA methods to refine alignments. However, multiple structural superposition is dependent on alignments, and a superposition generated based on erroneous alignments is not guaranteed to be the optimal superposition. Correcting errors after blackmaking errors is not as good as avoiding errors from the beginning. Hence it is important to refine the pairwise library to reduce the number of conflicts before any consistency-based assembly.

Results: We present an algorithm, Iterative Refinement of Induced Structural alignment (IRIS), to refine the PAL. A new measurement for the consistency of a library is also proposed. Experiments show that our algorithm can greatly improve T-COFFEE performance for less consistent pairwise alignment libraries. The final multiple alignment outperforms most state-of-the-art MSTA algorithms at assembling 15 transglycosidases. Results on three other benchmarks showed that the algorithm consistently improves multiple alignment performance.

Availability: The C++ code of the algorithm is available upon request.

Associate Editor: Anna Tramontano
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