A General Framework for Exact Partially Local Alignments

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.