From davide.rambaldi at ifom-ieo-campus.it  Wed Mar 23 12:23:42 2005
From: davide.rambaldi at ifom-ieo-campus.it (rambaldi)
Date: Wed Mar 23 12:18:25 2005
Subject: [Bioperl-microarray] Modules to handle affymetrix annotation tables
Message-ID: <5ad849842c330cc69370c58a2ca50c75@ifom-ieo-campus.it>

Hi, I am a young researcher and Perl developer of the IFOM-FIRC 
Institute of Cancer Research (Milan)
In the last month i have worked on a Perl module to handle Affymetrix 
Probesets Informations and store it in a Relational Database

Actually I have an account at PAUSE as RAMBALDI but i would like to add 
my modules to the BioPerl Bundle
Under CPAN search i FIND actualy only 2 packages

bioperl-microarray-0.1
Bio-Affymetrix-0.3

that work with Affymetrix Mass Fille.


My Package handle information about probesets design, alignments oligos 
ecc... and generate new data about single probes position over RefSeq 
and Genome.

Actually a web-interface to my modules are avaible at

http://bio.ifom-firc.it/AffyDB/

Just type 'random' into the INPUT BOX to get a random list of 10 
probesets

I would like to integrate my modules in the BioPerl distribution

I have used OOPerl and the template of 'Mastering Perl for 
Bioinformatics (Gene.pm)'

Actualy i have 2 modules called:

AffyDB.pm

parse annotation tables, insert tables into a Entity Relationship mySQL 
database, retrive informations

Probeset.pm

Really similar to Gene.pm, is an OOPerl module to create an object 
(Probeset) and handle informations about design, alignments, ecc...

And some perl CGI scripts to generate the web interface.

Perl DOCs about the 2 modules are available (html version) at

http://bio.ifom-firc.it/AffyDB/src/AffyDB.html

http://bio.ifom-firc.it/AffyDB/src/Probeset.html
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