[Bioperl-l] about gene "boundaries"

Dimitar Kenanov dimitark at bii.a-star.edu.sg
Thu Apr 29 00:48:20 EDT 2010


Hi guys,
today with rested head and after some reading i found the solution to my 
problem in BioPerl. Its Bio::DB::Fasta. It does what i want sufficiently 
well.
Thank you again for the help and im sorry for the trouble caused.

Cheers
Dimitar

On 04/28/2010 11:10 PM, Chris Fields wrote:
> By local DB, do you mean a BioPerl-based local DB?  Or is it something else?  This is a bit vague.
>
> On the BioPerl side I suggest looking into Bio::DB::SeqFeature::Store for storing and querying genome information (it does exactly what you want if the proper information is loaded), or maybe the Ensembl Perl API, which can be used with a local or remote Ensembl setup.  Beyond that you'll need to be more specific.
>
> chris
>
> On Apr 28, 2010, at 8:17 AM, 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.
>>
>> Thanks for any tips :)
>>
>> Cheers
>> Dimitar
>>
>> -- 
>> Dimitar Kenanov
>> Postdoctoral research fellow
>> Protein Sequence Analysis Group
>> Bioinformatics Institute
>> A*STAR, Singapore
>> email: dimitark at bii.a-star.edu.sg
>> tel: +65 6478 8514
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>      
>    


-- 
Dimitar Kenanov
Postdoctoral research fellow
Protein Sequence Analysis Group
Bioinformatics Institute
A*STAR, Singapore
email: dimitark at bii.a-star.edu.sg
tel: +65 6478 8514



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