[ensembl-dev] question on protein domains

[Nathalie Conte]

HI,
I am trying to retrieve the domain ID corresponding to a slice 
(chromosome, start,end) using ensembl API .
Here is how I get my domains, using the ensembl APIs- My starting point 
is a slice, where I get all the genes from, then the transcripts, then 
the translation and domains.

my $mouse_query_slice = 
$mouse_slice_adaptor->fetch_by_region('chromosome',$non_ref_seq_region,
     $non_ref_start,$non_ref_end);
my $all_genes=$gene_adaptor->fetch_all_by_Slice($mouse_query_slice);

if (scalar(@$all_genes)) {
print_genes($all_genes);
foreach my $ovegen(@{$all_genes}){
print "\t",
my @transcripts = @{ $ovegen->get_all_Transcripts };
my $transcript;
foreach  $transcript (@transcripts){
my $translation = $transcript->translation();
if ($translation) {
  my @domain_feats = @{$translation->get_all_DomainFeatures};
my $dom;
foreach $dom(@domain_feats){
     print 'transcript'.$transcript->stable_id.'-'.'domain 
ID'.$dom->hseqname.",";
     }
print  "\n";
                } else {
                  print 
'transcript'.$transcript->stable_id.'-'."Pseudogene\n";
                }

                                         }
}

and the output looks like this:
Bio::EnsEMBL::Transcript=HASH(0x49ae4b0)transcriptENSMUST00000118364-domain 
ID PS50853,transcriptENSMUST00000118364-domain ID SSF49265,
transcriptENSMUST00000118364-dommain ID 
SSF49265,transcriptENSMUST00000118364-domain ID PF09240,


 From this I have 2 questions:
1-First in the output, I get the $dom->hseqname() , it will display the 
id- PS50853, the is the domain ID from the PROSITE database.  I was 
wondering if there is a method to display the description of this domain 
like Fibronectin type-III domain profile?
2-Secondely, my starting point is a slice where I want my domain to be 
from. The way I am accessing the domain is through all genes  , where I 
get all the genes from, then the transcripts, then the translation and 
domains.
The problem with this is that I am going to get all the domains 
corresponding to the protein features not only the ones corresponding to 
this particular slice (could be 1 bp in size).

Could you suggest something?

Many thanks
Nathalie




-- 
Nathalie Conte, PhD
Bioinformatician BMB (WP3, WP7)
Functional Genomics group
EMBL-EBI,UK
01223 492562