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High speed BLASTN: an accelerated MegaBLAST search tool
Ying Chen1, Weicai Ye1, Yongdong Zhang2
1Guangdong Province Key Laboratory of Computational Science, School of Mathematics and Computational Science, Sun Yat-sen University, Guangzhou 510275, P. R. China.
Nucleic Acids Research
|August 8, 2015
Summary
High Speed BLASTN (HS-BLASTN) accelerates nucleotide database searches by using an FMD-index and seeding method. This bioinformatics tool is 22x faster than MegaBLAST, producing identical alignment results with improved parallel performance.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Sequence alignment is a fundamental bioinformatics task.
- The Basic Local Alignment Search Tool (BLAST) is widely used for sequence alignment.
- Increasing biological sequence data necessitates faster alignment tools.
Purpose of the Study:
- To develop a high-speed nucleotide alignment tool.
- To accelerate the MegaBLAST module within NCBI-BLASTN.
- To provide a parallel and efficient solution for large-scale sequence searches.
Main Methods:
- Developed High Speed BLASTN (HS-BLASTN), a parallel nucleotide database search tool.
- Utilized the FM-index for constructing a new database lookup table.
- Employed an accurate seeding method to identify short identical sequence regions (seeds).
Main Results:
- HS-BLASTN achieves the same alignment outcomes as MegaBLAST.
- HS-BLASTN demonstrates significantly faster computational speed, up to 22x faster than MegaBLAST on a 12-core server.
- Exhibits superior parallel performance compared to MegaBLAST.
Conclusions:
- HS-BLASTN offers a substantial speedup for nucleotide database searches.
- The tool maintains alignment accuracy while enhancing performance.
- HS-BLASTN is a viable, faster alternative to MegaBLAST for large biological sequence datasets.
