[Bioperl-l] about gene "boundaries"

Cook, Malcolm MEC at stowers.org
Fri Apr 30 10:16:59 EDT 2010


Dimitar,

Since you have indexed your database with makeblastdb, you might simply use `blastdbcmd` to extract, in fasta format, sub-sequences from the indexed database using identifiers and integer ranges 

blastdbcmd is included in the blast+ suite of programs, which also included makeblastdb which you report you have running.
  
see: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/user_maual.pdf

I've not (yet) used the blast+ suite (still using the old blast) so I've not tested this myself yet, but I think something like the following will work for you:

blastdbcmd -db yourBlastDatabase -entry  chr2 -range 100-300 -outformat fasta

will extract chr2:100-300 from yourBlastDatabase 

Good Luck

 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dimitar Kenanov
Sent: Wednesday, April 28, 2010 11:48 PM
To: Chris Fields; bioperl-l at bioperl.org; scott at scottcain.net; hrh at fmi.ch
Subject: Re: [Bioperl-l] about gene "boundaries"

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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