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2015 ; 43
(16
): 7762-8
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High speed BLASTN: an accelerated MegaBLAST search tool
#MMPMID26250111
Chen Y
; Ye W
; Zhang Y
; Xu Y
Nucleic Acids Res
2015[Sep]; 43
(16
): 7762-8
PMID26250111
show ga
Sequence alignment is a long standing problem in bioinformatics. The Basic Local
Alignment Search Tool (BLAST) is one of the most popular and fundamental
alignment tools. The explosive growth of biological sequences calls for speedup
of sequence alignment tools such as BLAST. To this end, we develop high speed
BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that
accelerates MegaBLAST--the default module of NCBI-BLASTN. HS-BLASTN builds a new
lookup table using the FMD-index of the database and employs an accurate and
effective seeding method to find short stretches of identities (called seeds)
between the query and the database. HS-BLASTN produces the same alignment results
as MegaBLAST and its computational speed is much faster than MegaBLAST.
Specifically, our experiments conducted on a 12-core server show that HS-BLASTN
can be 22 times faster than MegaBLAST and exhibits better parallel performance
than MegaBLAST. HS-BLASTN is written in C++ and the related source code is
available at https://github.com/chenying2016/queries under the GPLv3 license.