sudo apt-get install ncbi-blast+Linux/Unix Cluster:
# download sources wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.28+-x64-linux.tar.gz # unpack sources tar -xvzf ncbi-blast-2.2.28+-x64-linux.tar.gzNow the BLAST executables are located in
ncbi-blast-2.2.28+/bin
. Make sure to include the complete path when calling any BLAST executable, e.g.:
/home/digga/src/ncbi-blast-2.2.28+/bin/blastn [...]
(By the time this HOWTO was written 2.2.28 was the latest version. Make sure that you change the version number to the latest one when donloading BLAST.)
What sequences should the input be mapped to?
nt
database:
# choose an appropriate location for the database files cd ~/blastdb # download database files update_blastdb nt # unpack database files for f in nt.??.tar.gz do tar -xvzf $f done
# choose an appropriate location for the database files cd ~/blastdb # download FASTA files wget wget http://www.arb-silva.de/fileadmin/silva_databases/release_115/Exports/SSURef_NR99_115_tax_silva.fasta.tgz # unpack database file tar -xvzf SSURef_NR99_115_tax_silva.fasta.tgz # format FASTA sequences for use as BLAST db makeblastdb -in SSURef_NR99_115_tax_silva.fasta -dbtype nucl -out silva_ssu
blastn -query SSURef_NR99_115_tax_silva.fasta \ -db ~/blastdb/silva_ssu \ -out blast_results \ -outfmt 6 \ -num_threads 8