[Bioclusters] Web BLAST

Jeremy Mann bioclusters@bioinformatics.org
Wed, 20 Nov 2002 09:13:22 -0600 (CST)

> Hi Jeremy,
> I have been running a wwwblast server for more than a year now. Here is
> what you need to add in blast.rc.
> blastn     dna files
> blastp     protein files
> blastx     protein files
> tblastn    dna files
> tblastx    dna files
> The rest is quite simple but let us know if you have any more problems?

Just a couple more questions..... Another researcher looked over the
installation and did a couple BLAST runs. According to him, the blast that
comes with wwwblast is pretty old and the databases are formatted to what
NCBI used 5 years ago. Does NCBI use the same databases as what they
release to us?

If the database continues to be a problem, we also have the complete GCG
database available. Since BLAST wants its database in its own format, how
hard would it be to take the flat files from Genbank, format to FASTA,
then format to NCBI (using formatdb)? Or is this even possible?

Jeremy Mann

University of Texas Health Science Center
Bioinformatics Core Facility
Phone: (210) 567-2672