[Bioperl-l] about gene "boundaries"
dimitark at bii.a-star.edu.sg
Wed May 5 07:06:04 UTC 2010
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.
On 04/30/2010 10:16 PM, Cook, Malcolm wrote:
> 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.
> 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
> 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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