[Bioperl-l] about gene "boundaries"

[Dimitar Kenanov]

Hi guys,
thank you for your help. Im sorry i missed to give the information about 
the DB i have. Ok, i have DB of human genome which is only the reference 
genome organized in chromosomes in fasta format. Then formatted with the 
makeblastdb provided with blast+.
I will now go and read about the suggestions you provided and hopefully 
i solve the problem. Otherwise i suppose i have to parse the DB and 
search for the appropriate positions 'manually'.

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
>>
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>>      
>    


-- 
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