Name
Abstract | ||
|---|---|---|
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.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.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. |
Year | DOI | Venue |
|---|---|---|
2008 | 10.1093/bioinformatics/btn281 | ECCB |
Keywords | Field | DocType |
consistency idea,progressive alignment strategy,graph-based alignment,consistency notion,alignment accuracy,alignment tool,multiple genomic sequence,dna sequence,segment-based multiple sequence alignment,multiple sequence alignment tool,amino acid,multiple sequence alignment,computer science,genome sequence | Sequence alignment,Data mining,Graph,Alignment-free sequence analysis,Computer science,Theoretical computer science,Software,Bioinformatics,Multiple sequence alignment,Sequence analysis | Conference |
Volume | Issue | ISSN |
24 | 16 | 1367-4811 |
Citations | PageRank | References |
16 | 1.45 | 18 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Tobias Rausch | 1 | 262 | 18.00 |
| Anne-katrin Emde | 2 | 101 | 6.06 |
| David Weese | 3 | 252 | 17.79 |
| Andreas Döring | 4 | 195 | 19.38 |
| Cedric Notredame | 5 | 100 | 6.94 |
| Knut Reinert | 6 | 1020 | 105.87 |