how to set up a small EST database

Cornelius Krasel krasel at wpxx02.toxi.uni-wuerzburg.de
Fri Jul 27 05:49:58 EST 2001


Ricky Boernke <ricky_boernke at gmx.net> wrote:
> we have prepared a cDNA library of our favorite tissue and are now in
> the process of generating about 1.000 ESTs from that library. We
> were wondering if there is any possibility for a person not very much
> experienced in bioinformatics to set up a database for those sequences.

I would annotate all the sequence files and drop them into a directory.
You can search them with e.g. GCG (database is /path/to/directory/*)
and use standard unix tools (grep) to find any keyword in the headers.
I have not played with the free implementations of fasta or BLAST for
a while; therefore I don't know whether it is possible to use a list of
files in a directory for a database with them.

--Cornelius.

-- 
/* Cornelius Krasel, U Wuerzburg, Dept. of Pharmacology, Versbacher Str. 9 */
/* D-97078 Wuerzburg, Germany   email: krasel at wpxx02.toxi.uni-wuerzburg.de */
/* "Science is the game we play with God to find out what His rules are."  */




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