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<div class="moz-cite-prefix">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.<br>
<br>
M<br>
<br>
<br>
On 30/08/12 15:07, Michael Paulini wrote:<br>
</div>
<blockquote cite="mid:503F738D.8090605@sanger.ac.uk" type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">Have a look here: <a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Homology.html">http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Homology.html</a>
there you can find the documentation to the methods.
M
On 30/08/12 14:05, Yuan Chen wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">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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