Bioperl-guts: GFIT_0.01 (alpha version)

Hidemasa BONO bono@kuicr.kyoto-u.ac.jp
Wed, 24 Mar 1999 02:12:25 +0900 (JST)


To all bioperler,

I have just put my modules and scripts, named GFIT, for gene function
identification in bioperl ftp site(ftp://bio.perl.org/pub/hbono/).
These modules and scripts are now used for assigning EC numbers of
the genes in our KEGG project(http://www.genome.ad.jp/kegg/).
It is alpha-version.

The script, osearch, cuts multiple queries, and then calls fasta3_t
or ssearch3_t. And the script, otable, generates html report of
the search including bi-directional best hit information. 
When gene A in query set is most similar to gene B in an organism in
the database, and when gene B is most similar to gene A in query set,
we call it `bi-directional best hit'. And gene A and gene B are
assumed to be orthologous. In the result this orthologous relation
are indicated in red and yellow characters(the hits other than
bi-directional best hits are indicated in black characters). 

It can be used separately with KEGG systems, but the database for 
it is required. These databases can be obtained from my web server
(http://bono.kuicr.kyoto-u.ac.jp/GFIT/db/).
Because it has been developed tightly with KEGG, something might be
wrong without KEGG. Please report me any troubles. 

All scripts were tested under ORIGIN2000 running IRIX 6.4 with perl5.005_02.

Hidemasa
-=-=-=-=-=-=-
Hidemasa Bono, JSPS Research Fellow.
Institute for Chemical Research, Kyoto Univ.
mailto: bono@kuicr.kyoto-u.ac.jp
http://bono.kuicr.kyoto-u.ac.jp/ (URL was changed on this March)
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