Journal Article

Segment-based multiple sequence alignment

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

in Bioinformatics

Volume 24, issue 16, pages i187-i192
Published in print August 2008 | ISSN: 1367-4803
Published online August 2008 | e-ISSN: 1460-2059 | DOI:
Segment-based multiple sequence alignment

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  • Bioinformatics and Computational Biology


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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 A novel version of T-Coffee interfaced with the tool is available from The usage of the tool is described in both documentations.


Journal Article.  5016 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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