[ensembl-dev] a question about dN and dS

Michael Paulini mh6 at sanger.ac.uk
Thu Aug 30 14:17:00 BST 2012


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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