[Bioperl-l] Database Retrieval

[Chris Fields]

This was brought up previously:

http://article.gmane.org/gmane.comp.lang.perl.bio.general/11808/ 
match=ucsc

Would be nice to get something up and running here, even if it just  
returned raw data (not objects).  The more access the better.

In a similar vein, I developed Bio::DB::EUtiities to fetch raw data,  
like sequences, XML, etc, from any NCBI Entrez database as an  
alternative to using Bioperl objects; it could be used via an I/O  
module (like SeqIO) to convert said data into Bioperl objects or just  
return it unmodified by using it directly.  Still needs some work,  
just haven't had time lately.

BTW, you can use a 'slice adaptor' via GenBank files as well, both  
via Bio::DB::GenBank and Bio::DB::EUtilities.  They both accept the  
parameters seq_start, seq_stop, and strand, and both return the  
sequence slice containing relevant seqfeatures, etc for the region.

Chris

On Aug 7, 2006, at 10:51 AM, Sendu Bala wrote:

> Rick Scavetta wrote:
>> Hello Programmers,
>>
>> I have a list of mouse GeneIDs for which I have extracted the  
>> RefSeqs for.
>> With these accession numbers I want to know what are the three  
>> closest
>> upstream and downstream genes (and orientation, if possible) to my  
>> gene of
>> interest. Is these some way of finding this out? Any suggestions?
>
> One possible way would be with the Ensembl Perl API:
> http://www.ensembl.org/info/software/core/core_tutorial.html
>
> You'd get a gene or transcript adapator and use
> fetch_all_by_external_name() iirc.
>
> Then probably your slice adaptor would be used to get the up and down
> stream regions and iirc there's some easy way to ask for all the genes
> in a slice.
>
> Sean's solution (use UCSC) seems a lot easier, and since you just  
> want a
> list of names as a result, not bioperl objects, I'd go for that.
>
> Actually, would there be any interest in a bioperl interface to the  
> UCSC
> tables? It could probably be done using their DAS server, and end  
> up as
> a very easy-to-use alternative to the Ensembl API for limited or  
> one-off
> queries.
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign