[Bioperl-l] How to get the intron phase

Filipe Garrett fgarret at ub.edu
Fri Jul 8 10:39:21 EDT 2005

Hi all,

I'm new to bioperl and I was looking for a way to obtain the intron 
phases from genes in a FASTA format like this:

 >CG3427-RA type=transcript; 
ID=CG3427-RA; name=Epac-RA; 
release=r4.1; species=dmel; len=4028

I've looked at the script directory and found the phase method inside 
the Bio::SeqFeature::Gene::Intron object, but the examples are from data 
parsed from a GFF file.

Can I bypass the GFF stuff and use the FASTA header information directly?

Thanks in advance,


More information about the Bioperl-l mailing list