(Altschul et al. 1990 & 1997)

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 homepage


Blast online webtools

https://blast.ncbi.nlm.nih.gov/BlastSearch → help.pdf guide




→ Install Blast locally

Blast FAQ



→ E-Value & Bit-score

→ Word-size

Blast results

blastn -query genes.fasta -subject genome.fasta -outfmt 6

→ BLASTn output format 6

Blast database

makeblastdb -in ecoli.fasta -parse_seqids -dbtype nucl

→ Create BLAST database

Alternative tools

→ Bowtie2 to map short reads (shotgun sequencing) against reference genomes

→ FastANI to compare (draft) genomes by Average Nucleotide Identity (ANI)

read more

Altschul et al. 1990

Altschul et al. 1997