[ensembl-dev] a question about dN and dS

[Michael Paulini]

as far as I interpret it, it is the total number of nonsynonymous bases
it the alignment, so you can get a maximum of
size-of-alignment-block*number-of-sequences.
It can't be the average, as it returns integers .... that is unless it
rounds them.

But there is a $homology->dn method, that returns the nonsynonymous
substitution rate ... as in: the average rate per bp.


M

On 30/08/12 14:51, Yuan Chen wrote:
> 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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