[Bioperl-l] Fasta Genome Splice

[David Clark]

Good point.  What I need is two fasta files: one with the ofr regions 
masked, and one with the non-ofr regions masked.  There was another 
thing I wanted to do that I didn't mention before: how can I generate 
the reverse compliment of a whole genome file?

On Feb 12, 2004, at 1:19 PM, Jason Stajich wrote:

> You want these as a fasta file per orf and per non-orf region or just 2
> datasets with the genome masked (all N's or lowercased)?
>
> -jason
> On Thu, 12 Feb 2004, David Clark wrote:
>
>> Hello,
>>
>> I'm a relative newcomer to bioperl, and would like a point in the 
>> right
>> direction.  I need to separate the yeast genome into two partial
>> genomes--one with all ORF's, and one with everything else.  I have a
>> tab delimited list of the ORF's with the coordinates, and can probably
>> parse that myself, but I wanted to see if anyone could point me to 
>> some
>> example code, or give me some place to start in separating genomes
>> based on the coordinates.
>>
>> Thanks,
>>
>> David Clark
>> dfclark at neo.tamu.edu