The BLAST program is run on the command line on Discovery. You must have an account on Discovery in order to use BLAST. Please contact the Research Computing group at Research.Computing@dartmouth.edu to obtain an account.
The minimal requirements to run a BLAST search are a query sequence file, the database you are searching, and an output file name.
$ blastn -query YourInputFileHere -db /idata/appdata/blastdb/BlastDbNameHere -out YourOutputFileHere
In order to run any BLAST search on Discovery, you must first load the BLAST module.
$ module load blast+ $ blastn -query il2.seq -db /idata/appdata/blastdb/refseq_rna -out il2.blastn
In the command above, there are three pieces of information supplied to the blastn program. Blastn runs a nucleotide sequence against a nucleotide database. The three pieces of information are:
-query
-db
-out
-query
The -query parameter specifies the name of the file containing your query sequence, the sequence you want to use to search against the database. The query sequence must be in either FASTA or Genbank format. In this example, the name of the query file is il2.seq.
-db
The -db parameter specifies the name of the database you are going to run against. In this example the search is being run against the NCBI transcript reference sequences, refseq_rna.
-out
The -out parameter specifies the name of the file that will contain the search results. In this example we have named the output file il2.blastn.