[ensembl-dev] a question about dN and dS

[Yuan Chen]

Dear Michael,
In document, it said "number of nonsynonymous positions for the homology"

Suppose the homology consist of 10 species, is the average number (i.e total number of nonsynonymous changes devided by number of species) or just total number of nonsynonymous positions ?

As the n or s is not a integer, it's a decimal number, so I thought it would be some kind of average number ?

Thanks

yuan
On 30 Aug 2012, at 14:17, Michael Paulini wrote:

> Have a look here: http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Homology.html
> 
> there you can find the documentation to the methods.
> 
> M
> 
> 
> On 30/08/12 14:05, Yuan Chen wrote:
>> 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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>> 
>> 
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