[Bioperl-l] about gene "boundaries"
dimitark at bii.a-star.edu.sg
Wed Apr 28 22:04:15 EDT 2010
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'.
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.
> 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 :)
>> 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
Postdoctoral research fellow
Protein Sequence Analysis Group
email: dimitark at bii.a-star.edu.sg
tel: +65 6478 8514
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