Authors:
Falco Kirchner
1
;
Nancy Retzlaff
1
;
2
and
Peter F. Stadler
3
;
2
;
4
;
1
Affiliations:
1
Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, and Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
;
2
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
;
3
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
;
4
Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, U.S.A.
Keyword(s):
Multiple Sequence Alignments, Dynamics Programming.
Abstract:
Multiple sequence alignments are a crucial intermediate step in a plethora of data analysis workflows in computational biology. While multiple sequence alignments are usually constructed with the help of heuristic approximations, exact pairwise alignments are readily computed by dynamic programming algorithms. In the pairwise case, local, global, and semi-global alignments are distinguished, with key applications in pattern discovery, gene comparison, and homology search, respectively. With increasing computing power, exact alignments of triples and even quadruples of sequences have become feasible and recent applications e.g. in the context of breakpoint discovery have shown that mixed local/global multiple alignments can be of practical interest. vaPLA is the first implementation of partially local multiple alignments of a few sequences and provides convenient access to this family of specialized alignment algorithms.