[ensembl-dev] a question about dN and dS

Matthieu Muffato muffato at ebi.ac.uk
Thu Aug 30 09:16:25 BST 2012


Dear Mei

It seems that you are querying a fruit-fly gene. Unfortunately, the 
dN/dS values are only computed for close enough species: mammals, 
reptiles, and tetraodontiformes.

Nevertheless, your script is correct and would print some values if you 
use a human gene as query

Regards,
Matthieu

On 30/08/12 01:49, JiangMei wrote:
> Hi All.
>
> Sorry to bother you. I'm trying to use ensembl-compara (database version
> 67) to extract the homologues. I also want to get the dN, dS and dN/dS.
> However, ENSEMBL can't output these values. Can anyone help me?
>
> The following is the script I used:
>
> use Bio::EnsEMBL::Registry;
> my $registry = 'Bio::EnsEMBL::Registry';
> $registry->load_registry_from_db(
>        -host       =>'ensembldb.ensembl.org',
>        -user       =>'anonymous',
>        -db_version =>'67');
> my $member_adaptor=$registry->get_adaptor('Multi','compara','Member');
> my
> $member=$member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE','FBgn0002780');
> my $homology_adaptor=$registry->get_adaptor('Multi','compara','Homology');
> my $homologies=$homology_adaptor->fetch_all_by_Member($member);
>
> for $homology(@{$hom ologies}){
>      for $mem(@{$homology->get_all_Members}){
>          my $taxon=$mem->taxon; #check Bio::EnsEMBL::Compara::NCBITaxon
> for methods
>          my $id=$mem->stable_id;
>          print "$id\t",$taxon->taxon_id,"\t",$taxon->genus,"
> ",$taxon->species,"\t";
>       }
>      print $homology->description,"\t",$homology->subtype,"\t";
>      my $dn=$homology->dn;
>      my $ds=$homology->ds;
>      my $dnds=$homology->dnds_ratio;
>      my $lnl=$homology->lnl;
>      ($dn)?print "$dn\t$ds\t$dnds\t$lnl\n":print OUT "NA\tNA\tNA\tNA\n";
> }
>
>
> Wish your help! Thanks very much in advance!
>
>
> Best, Mei
>




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