Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

ABSTRACT:

Background

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations.

Results

A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 b

SUBMITTER: Daily J 

PROVIDER: S-EPMC4748600 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature