Sep 3, 2016

SWORD-a highly efficient protein database search

Bioinformatics
Robert VaserMile Šikić

Abstract

Protein database search is one of the fundamental problems in bioinformatics. For decades, it has been explored and solved using different exact and heuristic approaches. However, exponential growth of data in recent years has brought significant challenges in improving already existing algorithms. BLAST has been the most successful tool for protein database search, but is also becoming a bottleneck in many applications. Due to that, many different approaches have been developed to complement or replace it. In this article, we present SWORD, an efficient protein database search implementation that runs 8-16 times faster than BLAST in the sensitive mode and up to 68 times faster in the fast and less accurate mode. It is designed to be used in nearly all database search environments, but is especially suitable for large databases. Its sensitivity exceeds that of BLAST for majority of input datasets and provides guaranteed optimal alignments. Sword is freely available for download from https://github.com/rvaser/sword robert.vaser@fer.hr and mile.sikic@fer.hr Supplementary data are available at Bioinformatics online.

  • References11
  • Citations1

Citations

Mentioned in this Paper

Heuristics
Basic Local Alignment Search Tool
Environment
Bio-Informatics
Computer Programs and Programming
Protein Structure Databases
Bnk protein, Drosophila
Approach
Search Engine
Determination, Sequence Homology

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