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Journal Article

Segment-based multiple sequence alignment

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Rausch,  Tobias
IMPRS for Computational Biology and Scientific Computing - IMPRS-CBSC (Kirsten Kelleher), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Emde,  Anne-Katrin
Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Rausch, T., Emde, A.-K., Weese, D., Döring, A., Notredame, C., & Reinert, K. (2008). Segment-based multiple sequence alignment. Bioinformatics, 24(16):(16), i187-i192. doi:10.1093/bioinformatics/btn281.


Cite as: https://hdl.handle.net/11858/00-001M-0000-0010-80B1-C
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.