Segment-based multiple sequence alignment.
BACKGROUND
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.


BACKGROUND
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.
Rausch
Tobias
T
International Max Planck Research School for Computational Biology and Scientific Computing, Ihnestr 63-73, 14195 Berlin, Germany. rausch@inf.fu-berlin.de
Emde
Anne-Katrin
AK
Weese
David
D
Döring
Andreas
A
Notredame
Cedric
C
Reinert
Knut
K
D000465:Algorithms; D016415:Sequence Alignment / Q000379:methods*; D017421:Sequence Analysis / Q000379:methods*; D012984:Software