how to set up a small EST database

Francis Durst francis.durst at bota-ulpnospam.u-strasbg.fr
Mon Jul 30 13:03:02 EST 2001


In article <3B612139.8B29DBEF at gmx.net> Ricky Boernke <ricky_boernke at gmx.net> writes:
>From: Ricky Boernke <ricky_boernke at gmx.net>
>Subject: how to set up a small EST database
>Date: Fri, 27 Jul 2001 10:07:21 +0200

>Dear friends,

>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.
>This database should be searchable for sequence homologies and by
>keywords, i.e. enzyme names.
>Any input appreciated.

>TIA
>Ricky

If all you need is a fast way to blast-search your ESTs,
the simplest way is to concatenate all seqs in one fasta file
(or GenBank format if you need more elaborate annotation
than the comments you can place on the first Fasta line
after the >name = about 240 characters). 
You can download stand-alone BLAST for IRIX6.2, Solaris2.6, 
DEC OSF1 (ver. 4.0d), LINUX, and Win32 systems from 
ftp://ncbi.nlm.nih.gov/blast/executables

You'll get a program to build a Blast readable database and
different flavors of Blast. It works fine.

If you have a PC, a very easy alternative is to download
BioEdit from http://jwbrown.mbio.ncsu.edu/BioEdit/bioedit.html

With BioEdit it is a snap to built the database and it has
a built-in facility to do local Blast (i.e. against your
own database(s). It is escellent.

All the best

Francis




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