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Bioinformatics Advance Access published online on October 6, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm485
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© 2007 The Author(s)
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.

Biclustering As A Method For RNA Local Multiple Sequence Alignment

Shu Wang 1,*, Robin R. Gutell 2 and Daniel P. Miranker 3

1Department of Electrical and Computer Engineering, 2 School of Biological Sciences, Section of Integrative Biology,and 3Department of Computer Science, University of Texas At Austin, Austin, TX 78712, USA

*To whom correspondence should be addressed. Shu Wang, E-mail: swang5{at}ece.utexas.edu


  Abstract

Motivation: Biclustering is a clustering method that simultaneously clusters both the domain and range of a relation. A challenge in multiple sequence alignment (MSA) is that the alignment of sequences is often intended to reveal groups of conserved functional subsequences. Simultaneously, the grouping of the sequences can impact the alignment; precisely the kind of dual situation biclustering is intended to address.

Results: We define a representation of the MSA problem enabling the application of biclustering algorithms. We develop a computer program for local MSA, BlockMSA, that combines biclustering with divide-and-conquer. BlockMSA simultaneously finds groups of similar sequences and locally aligns subsequences within them. Further alignment is accomplished by dividing both the set of sequences and their contents. The net result is both a multiple sequence alignment and a hierarchical clustering of the sequences.

Availability: BlockMSA is implemented in Java. Source code and supplementary data sets are available at http://aug.csres.utexas.edu/msa/.

Contact: swang5{at}ece.utexas.edu

Associate Editor: Prof. Keith Crandall

Received on April 21, 2007; revised on August 20, 2007; accepted on September 14, 2007

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A local multiple alignment method for detection of non-coding RNA sequences
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[Abstract] [Full Text] [PDF]


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