[ensembl-dev] a question about dN and dS

[Yuan Chen]

On the same line, can any one explain what is n and s obtained by :

$homology->n; $homology->s;

Is this a number of non_synonymous or synonymous changes for the gene ?

yuan
On 30 Aug 2012, at 09:16, Matthieu Muffato wrote:

> 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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