[ensembl-dev] a question about dN and dS

Michael Paulini mh6 at sanger.ac.uk
Thu Aug 30 15:46:00 BST 2012


I have to take that back, it is per pair and therefore the maximum N
should be 2*alignment size and is exact. Whereas the dN and dS is
estimated through PAML.

M


On 30/08/12 15:07, Michael Paulini wrote:
> 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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