Motivation

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.

Availability and Implementation

Sword is freely available for download from https://github.com/rvaser/sword

Contact

[email protected] and [email protected]

Supplementary information

Supplementary data are available at Bioinformatics online.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected]