SWORD—a highly efficient protein database search (CROSBI ID 648910)
Prilog sa skupa u časopisu | izvorni znanstveni rad | međunarodna recenzija
Podaci o odgovornosti
Vaser, Robert ; Pavlović, Dario ; Šikić, Mile
engleski
SWORD—a highly efficient protein database search
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
protein, sequence similarity search, alignment
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Podaci o prilogu
680-684.
2016.
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objavljeno
Podaci o matičnoj publikaciji
Bioinformatics
1367-4803
Podaci o skupu
ECCB 2016: THE 15TH EUROPEAN CONFERENCE ON COMPUTATIONAL BIOLOGY
predavanje
03.09.2016-09.09.2016
Den Haag, Nizozemska
Povezanost rada
Računarstvo, Biologija