SeqAn::T-Coffee

Abstract

SeqAn::T-Coffee is an open source multiple sequence alignment program. SeqAn::T-Coffee aligns aminoacid, DNA and RNA sequences using a consistency-based progressive alignment algorithm on a graph of sequence segments.

Please Cite

T. Rausch, A.-K. Emde, D. Weese, C. Notredame, K. Reinert, “Segment-based multiple sequence alignment”, vol. 24, iss. 16, 2008.

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@article{fu_mi_publications391,
 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@inf.fu-berlin.de},
 author = {T. Rausch and A.-K. Emde and D. Weese and C. Notredame and K. Reinert},
 journal = {Bioinformatics},
 number = {16},
 pages = {i187--192},
 title = {Segment-based multiple sequence alignment},
 url = {http://publications.imp.fu-berlin.de/391/},
 volume = {24},
 year = {2008}
}

Contact

For questions, comments, or suggestions please contact:

Tobias Rausch rausch@embl.de

Abstract

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