[Bioperl-l] Extraction of Intergenic region

[Jason Stajich]

[bioperl-l is really the right list to post to]

There isn't exactly something that does this, but you can write a 
script to do this by parsing the sequence file with Bio::SeqIO and the 
coordinate file.
Have you tried to write the simple perl to do this yet.  You can do it 
pretty basically with the substr function.  I also have done it where I 
mask the coding sequence with 'N's first then use split to go back and 
extract all the non-N regions.

-jason
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/
On Jan 27, 2005, at 4:32 AM, Rafi Ahmad wrote:

> Hi everyone,
>
> I am new to BioPerl. Would like to know that is there a BioPerl code 
> that helps extract intergenic sequences in a genome, given a 
> coordinate file mentioning the start and stop position of all the 
> genes.
>
> Thanks for the help.
>
> Regards
>
> Rafi
>
> _______________________________________________
> Bioperl-guts-l mailing list
> Bioperl-guts-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l
>