BLASTn

Create a database and search for homologues in nt fasta files and recover sequences from NCBI.

BLAST scheduleMarch 31, 2026

Make the Database

info

For output format options, see: https://www.biostars.org/p/161457/

makeblastdb -dbtype nucl -in Sequences.fna -input_type fasta

Run BLASTn

Run locally against a custom database:

blastn -db Sequences.fna -query 16S_sequences.fna -max_target_seqs 10 -out Blast_16S_Sequences.tab -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore" -word_size 5 -perc_identity 90 -num_threads 10

Run via SLURM against the nt database:

#!/bin/bash

#SBATCH --job-name=Blastn
#SBATCH --time=
#SBATCH --cpus-per-task=
#SBATCH --mem=
#SBATCH -w 
#SBATCH --partition=
#SBATCH --output=%x_%j_stdout.txt
#SBATCH --error=%x_%j_stderr.txt

#SBATCH --mail-type=ALL
#SBATCH --mail-user=


export PATH="/home/blast:$PATH"
blastn -db nt -query Sequences.faa -max_target_seqs 10 -out BLAST_Results.tab -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids" -word_size 5 -evalue 0.00001 -num_threads 15

Include the header in the first line of the BLAST results:

sed -i '1i qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids' Blast_Results.tab

info

Make sure to check if your table has the last column (Taxonomy information).

Recover Sequences from NCBI

Install Entrez:

#Create an environment in which you can add Entrez Direct
conda create --name entrez

#Activate this new environment
conda activate entrez

#Install Entrez
conda install -c bioconda entrez-direct

Create a list with the accession numbers of the sequences to recover:

nano list.txt

ABO08866.1
AFA39020.1
AFA39042.1
AFI78392.1
AOQ24367.1
APC08827.1
ATY72478.1

Change the file from a column to a CSV:

cat list.txt | tr "\n" "," | sed 's/,$//' > list.csv

Make an executable script:

sed 's/^/efetch -db protein -format fasta -id /' list.csv > list.sh

chmod +x list.sh

It should look like this:

efetch -db protein -format fasta -id ABO08866.1,AFA39020.1,AFA39042.1,AFI78392.1,AOQ24367.1,APC08827.1,ATY72478.1

Run the script:

bash list.sh > list.faa