[Bioperl-l] ensembl database

Stefan Kirov skirov at utk.edu
Wed Jul 28 07:13:59 EDT 2004

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;
The current server is ensembldb.ensembl.org.
See the ensembl API documentation for more help.
Hope this helps

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
> _________________________________________________________________
> Use MSN Messenger to send music and pics to your friends 
> http://www.msn.co.uk/messenger
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
1060 Commerce Park, Oak Ridge
TN 37830-8026
tel +865 576 5120
fax +865 241 1965
e-mail: skirov at utk.edu
sao at ornl.gov

More information about the Bioperl-l mailing list