Journal
NUCLEIC ACIDS RESEARCH
Volume 43, Issue 16, Pages 7762-7768Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkv784
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Funding
- Guangdong Provincial Government of China
- Natural Science Foundation of China [11471013]
- Fundamental Research Funds for the Central Universities [131gjc05, 141gjc01]
- Guangdong Province Sun Yat-sen University Education Development Foundation [305027]
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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 ext-link-type=uri xlink:href=https://github.com/chenying2016/queries>https://github.com/chenying2016/queries under the GPLv3 license.
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