[Bioperl-l] about gene "boundaries"

[Dimitar Kenanov]

Hi Malcolm,
thank you very much for that information. Didnt even know such program 
existed :) I now use 'blastdbcmd' for extraction of DNA sequence from my 
DB. I only had to reformat my DB with 'parse seqids' parameter in order 
to be able to give the 'entry' parameter to 'blastdbcmd'.

Now my script is working.
Thanx again.

Cheers
Dimitar


On 04/30/2010 10:16 PM, Cook, Malcolm wrote:
> 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
>
> _______________________________________________
> 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