[Bioperl-l] New to BioPerl - Gene prediction & fgenesh

Fields, Christopher J cjfields at illinois.edu
Tue Mar 27 13:14:08 EDT 2012


On Mar 27, 2012, at 9:29 AM, Merche Castillo wrote:

> Hi everyone,
> 
> I am working on gene prediction in nematodes and I'm interested in learning more about BioPerl and how I can use it to get some nice prediction out of my nematode contigs. I have already done some predictions with the Fgenesh web version, but it takes a long time since I have to submit each contig separately. Thus I'm interesting in writing a script that would use the fgenesh module. I have seen the documentation is quite old, so I wonder whether the BioPerl module runs on the latest version.

I'm not sure to tell the truth, but it shouldn't be terribly hard to update unless the API has changed significantly.  

> Since I would like to do comparative genomics among different nematode species I was wondering whether it is possible to find fgenesh+ or fgenesh++. Since I am quite new here I would appreciate any advice on BioPerl and gene prediction

Have you looked at the MAKER pipeline?  I understand it uses quite a few of the gene predictors (FGENESH included).

http://gmod.org/wiki/MAKER
http://www.yandell-lab.org/software/maker.html

It doesn't appear they use bioperl-run modules for these, though.

chris

> Thanks in advance
> 
> Best Regards
> 
> 
> -- 
> ************************************;)
> Mercedes Castillo
> INRES, Dept. Molecular Phytomedicine
> University of Bonn
> 
> Karlrobert-Kreiten-str 13
> 53115 Bonn
> +49(0)22873-60143
> merche at uni-bonn.de
> *****************************************
> 
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