[Bioperl-l] about gene "boundaries"

Hans-Rudolf Hotz hrh at fmi.ch
Wed Apr 28 10:13:37 EDT 2010



On 04/28/2010 03:17 PM, Dimitar Kenanov wrote:
> Hello guys,
> i have a question about gene "boundaries". Is there some module in
> BioPerl which can help me extract the DNA sequence from a genomic DB
> (from specific chromosome). I have my human genome in a local DB and
> some "from-to" data sets corresponding to different chromosomes. So i
> want to get the DNA seqs for these from-to's. I know i can do that the
> normal way but if there is a way to do it with BioPerl it will be more
> consistent with the rest of the code.


Dimitar

I don't know, what you call "the normal way"....although you apparently 
have the genome sequences locally already, I recommend to use the 
ensembl API to fetch genomic sequences (ie "from-to's").

see: http://www.ensembl.org/info/docs/api/core/core_tutorial.html

it is not BioPerl but a distant relative of it


Regards, Hans


> Thanks for any tips :)
>
> Cheers
> Dimitar
>


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