DIAMOND BLAST

Create a database and search for homologues in amino acid FASTA files.

BLAST codeGitHub languageManual menu_bookPaper scheduleApril 01, 2026

Installation

Downloading the tool

wget http://github.com/bbuchfink/diamond/releases/download/v2.1.9/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz

Add to PATH

export PATH=/Installation_folder:$PATH

Create a Database

Make sure both the query file (what will be searched) and the database file (where the query will be searched) contain amino acid sequences.

In case you need to convert your nucleotide sequences to amino acid sequences, run Prodigal first:

for i in *.fna ; do prodigal -i $i -o output.txt -a $i.faa ; done

To create the database, run:

diamond makedb --in aminoacids_sequences.faa --db generated_database

The input file is a FASTA file containing amino acid sequences (aminoacids_sequences.faa). It will generate a database file (generated_database.dmnd) that will be used as the search database.

Create the DB containing taxonomic info

diamond makedb --in /home/DB/DIAMOND_2022/NCBI_NR/nr.gz --db ncbi_nr_06-16-22 --taxonmap /home/Database/DIAMOND/prot.accession2taxid.FULL.gz --taxonnodes /home/Database/DIAMOND/nodes.dmp --taxonnames /home/Database/DIAMOND/names.dmp

Prepare the Query File

The output file from Prodigal (translated amino acid sequences) needs to be processed before being used in DIAMOND.

The first step is to delete all characters after the first space in the headers:

for i in *.faa; do sed -i 's/\s.*$//' $i; done

The * character should be deleted from the file:

for i in *.faa; do sed -i 's/*//g' $i; done

Then the sequences should be transformed to one-liners:

for i in *.faa ; do perl -lne 'if(/^(>.*)/){ $head=$1 } else { $fa{$head} .= $_ } END{ foreach $s (sort(keys(%fa))){ print "$s\n$fa{$s}\n" }}' $i >> $i.1L.faa ; done

A new file with the extension .1L.faa will be created in the directory. This file should be used as input in DIAMOND.

Run DIAMOND BLAST

diamond blastp --db generated_databasse.dmnd --query seqeunces2search.faa --out Results.tab --threads 3 --outfmt 6 qtitle stitle pident length qstart qend sstart send qlen slen qcovhsp scovhsp evalue bitscore --max-target-seqs 10 --evalue 0.000001 --id 30

Run recovering taxonomic information

/home/Database/DIAMOND/diamond blastp --db /home/Database/DIAMOND/ncbi_nr_06-16-22.dmnd --query seqeunces2search.faa --out Results.tab --threads 10 --outfmt 6 qtitle stitle pident length qstart qend sstart send evalue bitscore staxids sscinames sskingdoms skingdoms sphylums --max-target-seqs 3

Add the Header to Your Results

sed -i '1i\qtitle\tstitle\tpident\tlength\tqstart\tqend\tsstart\tsend\tqlen\tslen\tqcovhsp\tscovhsp\tevalue\tbitscore\tDB' Results.tab

Recover the Sequences from the Query

Get the header of the sequences in the results

for i in *.mcr ; do cut -f 1 $i > $i.txt ; done

Recover the sequences from the query

pullseq -i seqeunces2search.faa -n Header_of_interest.txt Recovered_sequences_of_interest.faa