High speed BLASTN: an accelerated MegaBLAST search tool

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…

• MS
  Memorial Sloan-Kettering Cancer Center

  Award: 11471013
• NN
  National Natural Science Foundation of China

  Award: 11471013
• SY
  Sun Yat-sen University
• GO
  Government of Jiangxi Province
• FR
  Fundamental Research Funds for the Central Universities

  Awards: 14lgjc01, 13lgjc05