[Bioperl-l] Database Retrieval

Alexander Kozik akozik at atgc.org
Mon Aug 7 12:13:39 EDT 2006


if a sorted list (table) of all genes is available for each orientation 
then simple 'grep' could help, e.g.:
$grep -A 2 -B 2 -f list_of_ids table_with_genes
where:
-A 2 tells to extract two lines below match
-B 2 two lines above match
list_of_ids - file with a list of genes of interest
table_with_genes - sorted by genome position table of all genes.

There is an assumption that genes on table are sorted according to their 
genome positions. It would be better to have two tables with sorted 
genes, one table per orientation (strand).

Alexander Kozik
Bioinformatics Specialist
Genome and Biomedical Sciences Facility
451 East Health Sciences Drive
University of California
Davis, CA 95616-8816
Phone: (530) 754-9127
email#1: akozik at atgc.org
email#2: akozik at gmail.com
web: http://www.atgc.org/


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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