LocalBlast
This is a description of how to perform a BLAST search on your local machine. Complete documentation can be found at NCBI.Install NCBI BLAST
Ubuntu: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.)
Target Database
What sequences should the input be mapped to?NCBI Database
Example: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
Custom Database
Example: SILVA database:# 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
Run BLAST
blastn -query SSURef_NR99_115_tax_silva.fasta \
-db ~/blastdb/silva_ssu \
-out blast_results \
-outfmt 6 \
-num_threads 8
Comments
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