BLAST - Metagenomics

Tools‎ > ‎

BLAST

(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
https://blast.ncbi.nlm.nih.gov/

Blast online webtools
https://blast.ncbi.nlm.nih.gov/BlastSearch
http://www.genome.jp/tools/blast/

http://web.expasy.org/blast/

→ Install Blast locally

Blast FAQ

https://blast.ncbi.nlm.nih.gov/blast/FAQ

Options

→ E-Value & Bit-score

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

www.metagenomics.wiki

Subpages (9): BLAST error: Too many positional arguments BLASTn output format 6 BLAST word-size BLASTx E-value & Bit-score FastANI Generate_database Install BLAST megablast