PT  - JOURNAL ARTICLE
AU  - Robert Vaser
AU  - Dario Pavlovi
AU  - Matija Korpar
AU  - Mile Sikic
TI  - SWORD - a highly efficient protein database search
AID  - 10.1101/014654
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 014654
4099  - http://biorxiv.org/content/early/2015/02/02/014654.short
4100  - http://biorxiv.org/content/early/2015/02/02/014654.full
AB  - 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 size in recent years has brought significant challenges in improving already existing algorithms. BLASTP 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 comple-ment or replace BLASTP. In this paper, we present SWORD, an efficient protein database search implementation that runs 3-4 faster than BLASTP in the sensitive mode and up to 18 faster in the fast and less accurate mode and also provides guaranteed optimal alignments for candidate sequences. SWORD is designed to be used in nearly all database search environments, but is especially suitable for large databases. Its sensitivity exceeds that of BLASTP for majority of input datasets.Availability Sword is freely available for download from https://github.com/rvaser/swordContact robert.vaser{at}fer.hr, mile.sikic{at}fer.hr