Questions on build Genbank files for Blast search

Stephane Bortzmeyer bortzmeyer at pasteur.fr
Fri Feb 26 04:56:37 EST 1999

In article <7aummr$jqn$1 at nnrp1.dejanews.com>,
 gmei at genetics.com writes:
> We are planning to build a local copy of Genbank database to do Blast search
> in house on an Alpha Digital Unix machine. We do not have GCG package and are
> not planning to buy it (at least for now).

We do the same and on the same machine/system. 
See <http://bioweb.pasteur.fr/seqanal/interfaces/blast2.html> on
how to use it remotely and what banks do we have.

> A. 1. Download Blast executable from NCBI and configure it 2. Download the
> "*.seq.Z" files from NCBI (ftp://ncbi.nlm.nih.gov/genbank/) 3. Uncompress
> them 4. Run some program (?) to convert file format to a GanBank file in
> Blast format 5. Run Blast 6. Download Genbank updates periodically and run
> some program (?) to "append" the update file to Genbank file.

We have developed in-house programs to do so. It is quite
complicated because you do not want the update to mess with the
current searches. AdvFs is useful there.

Ask Nicolas Joly <njoly at pasteur.fr>. I'm not sure about the legal
terms to distribute these programs. I'm fairly certain that the technical
terms are "It work for us, that's all we know". 

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