[Bioperl-l] GFF question

Jason Stajich jason.stajich at duke.edu
Mon Mar 7 13:51:09 EST 2005

All of the Parsers produce Bio::SeqFeatureI objects (well nearly all of 
them).  SeqFeatureI objects can be written out to GFF with 
Bio::Tools::GFF (and presumably Bio::FeatureIO).   Some of the 
genefeature parsers try and build Gene objects so you may have to 
untangle them some to get at the underlying exons and write each of 
those out to GFF as well.

There isn't a Repeatmasker parser in Bioperl that I know of although 
Ensembl has one which could be ported some day.

Jason Stajich
jason.stajich at duke.edu

On Mar 3, 2005, at 8:11 AM, Thiago Motta Venancio wrote:

> Hi folks.
> I would like to get a more detailed explanation about how to construct 
> GFF files with the outputs of several programs, like genescan, 
> repeatmasker...
> thanks in advance.
> Thiago
> -- 
> Thiago Motta Venancio - PhD student in Bioinformatics
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PGP.sig
Type: application/pgp-signature
Size: 186 bytes
Desc: This is a digitally signed message part
Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20050307/80368bda/PGP.bin

More information about the Bioperl-l mailing list