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Basic Local Alignment Search Tool (BLAST)

BLAST is a software tool for searching similarity in nucleotide sequences (DNA) and/or amino acid (protein) sequences.

  • similarity search of nucleotide or amino acid sequences
  • allows gaps (deletions and insertions)
  • local alignment: detect regions (subsequences) that are similar between two compared sequences
  • homology search of gene or protein sequences. For short read mapping see bowtie2 or BWA.

Blast download & install (local standalone blast search)
Blast FAQ


Blast results
blastn  -query genes.ffn  -subject genome.fna  -outfmt 6
→  BLASTn output format 6

Blast database
makeblastdb -in ecoli.fasta -parse_seqids -dbtype nucl