ArticleNucleic acids research2015
High speed BLASTN: an accelerated MegaBLAST search tool.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 444 papers.
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444 citing papers in PubMed.
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- Assembly and comparative analysis of the complete mitochondrial genome of Viola philippica (Malpighiales, Violaceae).Planta · 2026Article
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- Assembly and comparative analysis of the complete mitochondrial genome of Polygonatum odoratum (Yuzhu), a medicine-food homologous plant.BMC plant biology · 2026Article
- Phylogenomic conflict inPlant diversity · 2026Article
384 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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.
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