[Bioperl-l] ensembl database

[Stefan Kirov]

Why wouldn't you use ensembl API. It is great for exactly this type of 
stuff. Something like:
$hsdbadapt= new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host, -user => 
'anonymous', -dbname =>'homo_sapiens_core_21_34d',-pass=>'');
  my $slice_adaptor=$hsdbadapt->get_SliceAdaptor;
  my $slice = $slice_adaptor->fetch_by_chr_start_end($chr,$begin,$end);
  my @genes=@{$slice->get_all_Genes};
  foreach my $gene(@genes) {
    push @ids,$gene->stable_id;
  }
...etc.
The current server is ensembldb.ensembl.org.
See the ensembl API documentation for more help.
Hope this helps
Stefan

Stuart Gillies wrote:

> Hi, i am trying to write a bio perl script to query the ensembl 
> database. i am trying to retrieve data associated with a specific 
> region on the mouse genome chromosome 17: chr17:31,132,104-35,332,226. 
> i want a list of ensembl genes in that region, with as much info as 
> possible, such as transcription start point, ensembl gene ID,etc
>
> i also really need a list of conserved sequences (which should be 
> found in the compara database) for that mouse genomic region.
>
> any help would be great
>
> stuart gillies
>
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-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
1060 Commerce Park, Oak Ridge
TN 37830-8026
USA
tel +865 576 5120
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e-mail: skirov at utk.edu
sao at ornl.gov