[ensembl-dev] a question about dN and dS
Yuan Chen
yuan at sanger.ac.uk
Thu Aug 30 16:59:47 BST 2012
So do compara calculate number of synonymous change for the gene in paired species ? ie like human is ACG chimp is AGG, then you will count as one non-synonymous change, do you store this in database as n ?
if a homology consists more than 2 species, do you calculate multi pair species, than average as I do got n and s as decimal number, such as for gene : ENSG00000251258 n=543.5 s=245.5 ?
Thanks
yuan
On 30 Aug 2012, at 15:46, Michael Paulini wrote:
> 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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