April 17, 2006 - BLAST programs

I wanted to use the latest non redundant databases for my BLAST search. Do you provide access to the blast-formatted databases from the command line?

The latest non redundant databases are downloaded from NCBI once every month, and can be accessed from /bioportal/db/blast using your CGB Research Computing account. Also if you use the command 'use blastall'. you can directly use the name of the database in your BLAST query.

Example

blastall -i fasta_file -d nt -p blastn

Similarly the latest rel4.3 files for D melanogaster can also be used on CGB research.