[Bioclusters] Web BLAST

Andrew Shewmaker` bioclusters@bioinformatics.org
Wed, 20 Nov 2002 08:57:36 -0700

On Wed, 20 Nov 2002 09:13:22 -0600 (CST)
Jeremy Mann <jeremy@bioc09.v19.uthscsa.edu> wrote:

> 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?

I just installed a wwwblast server last week on a Solaris box and it 
didn't come with the blast program.  It is provided in a separate tarball 
although I think they used to be packaged together.  If yours were packaged 
together it may very well be an older version of blast.

Arshad has already replied and told you that the dbs NCBI provides are not 
old.  I checked the timestamps for the files in 
ftp://ftp.ncbi.nih.gov/blast/db/FormattedDatabases and they were modified 
just yesterday.  I formatted all of the dbs myself, so I don't have any 
actual experience with them to share with you.


Andrew Shewmaker
Associate Engineer
Phone:  208.526.1415
Fax:  208.526.4017

Idaho National Engineering and Environmental Laboratory
2525 Fremont Ave.
Idaho Falls, ID 83415-3605