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Bioinformatics 2008 24(16):i187-i192; doi:10.1093/bioinformatics/btn281
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Segment-based multiple sequence alignment

Tobias Rausch 1,*, Anne-Katrin Emde 2, David Weese 2, Andreas Döring 2, Cedric Notredame 3 and Knut Reinert 2

1International Max Planck Research School for Computational Biology and Scientific Computing, Ihnestr. 63-73, 14195 Berlin, Germany, 2Algorithmische Bioinformatik, Institut für Informatik, Takustr. 9, 14195 Berlin, Germany and 3Comparative Bioinformatics Group, Center for Genomic Regulation, Dr Aiguader 88, 08003 Barcelona, Spain

*To whom correspondence should be addressed.


  Abstract

Motivation: Many multiple sequence alignment tools have been developed in the past, progressing either in speed or alignment accuracy. Given the importance and wide-spread use of alignment tools, progress in both categories is a contribution to the community and has driven research in the field so far.

Results: We introduce a graph-based extension to the consistency-based, progressive alignment strategy. We apply the consistency notion to segments instead of single characters. The main problem we solve in this context is to define segments of the sequences in such a way that a graph-based alignment is possible. We implemented the algorithm using the SeqAn library and report results on amino acid and DNA sequences. The benefit of our approach is threefold: (1) sequences with conserved blocks can be rapidly aligned, (2) the implementation is conceptually easy, generic and fast and (3) the consistency idea can be extended to align multiple genomic sequences.

Availability: The segment-based multiple sequence alignment tool can be downloaded from http://www.seqan.de/projects/msa.html. A novel version of T-Coffee interfaced with the tool is available from http://www.tcoffee.org. The usage of the tool is described in both documentations.

Contact: rausch{at}inf.fu-berlin.de


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