[Bioperl-l] Extraction of Intergenic region

Jason Stajich jason.stajich at duke.edu
Thu Jan 27 18:13:51 EST 2005

[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 Stajich
jason.stajich at duke.edu
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
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