<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi,</div><div>Your module looks to be fine, I can find regions which report more than one score:</div><div>eg</div><div>20_70485_TCTT/- 20:70485-70488 - ENSG00000178591 ENST00000382410 Transcript intron_variant,feature_truncation - - - - - - Conservation=-0.557,-3.710,0.660,-0.666</div><div><br></div><div>To view on the web site:</div><div><a href="http://www.ensembl.org/Homo_sapiens/Location/View?db=core;r=20:70485-70488">http://www.ensembl.org/Homo_sapiens/Location/View?db=core;r=20:70485-70488</a></div><div><br></div><div>Is this what you were expecting? Not all positions in the alignment may have a score, if, for example, there are insufficient species in the alignment at that point:</div><div>eg</div><div>20_120591_AAGTC/- 20:120591-120595 - ENSG00000125788 ENST00000542572 Transcript upstream_gene_variant - - - - - - Conservation=0.114,0.114;DISTANCE=2680</div><div>Here only 2 of the 5 positions have a score and the 36 way eutherian alignment looks like:</div><div><a href="http://www.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=622;db=core;r=20:120591-120595">http://www.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=622;db=core;r=20:120591-120595</a></div><div><pre>Homo sapiens <span>AAGTC</span>
Pongo abelii <span>AA---</span>
Nomascus leucogenys <span>AAGTC</span>
Macaca mulatta <span>AA---</span></pre><div>Does that help?</div></div><div>Cheers</div><div>Kathryn</div><br><div apple-content-edited="true">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Kathryn Beal, PhD<br>European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Trust Genome Campus, Hinxton<br>Cambridge CB10 1SD, UK <br>Tel. +44 (0)1223 494458<br><a href="http://www.ensembl.org/">www.ensembl.org</a><br></div></div></div>
</div>
<br><div><div>On 3 Jun 2013, at 08:49, Guillermo Marco Puche wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type">
<div bgcolor="#FFFFFF" text="#000066">
<div class="moz-cite-prefix">Hello,<br>
<br>
Thank you very much for all this information. It has been really
helpful.<br>
<br>
Now I'm back to Conservation plugin code. I've modified it to
report the list of Conservation scores and not the average of all
(like the original plugin). However on all the tests I've
performed only one score is being reported. <br>
<br>
You can have a look at the code right here: <a href="https://github.com/guillermomarco/vep_plugins_71/blob/master/Conservation.pm">https://github.com/guillermomarco/vep_plugins_71/blob/master/Conservation.pm</a><br>
<br>
Modified lines from 165 to 180.<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 05/29/2013 02:43 PM, Stephen Fitzgerald wrote:<br>
</div>
<blockquote cite="mid:alpine.LRH.2.03.1305291310100.17764@ebi.ac.uk" type="cite">Hi Guillermo,
<br>
as a measure of conservation we display the ‘rejected
substitution' scores (accessed via the
$conservation_score->diff_score method in the compara API)
calculated by GERP.
<br>
The diff_score = expected_score - observed_score.
<br>
So, the more positive the diff_score is the more resistant to
substitutions
<br>
that column in the multiple alignment is (ie the more conserved it
is over evolutionary time). We do not have p-values for the
conservation scores. However, we do have p-values for the
constrained elements generated from the conservation scores.
<br>
<br>
Hope that helps,
<br>
Stephen.
<br>
<br>
<br>
On Wed, 29 May 2013, <a class="moz-txt-link-abbreviated" href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a> wrote:
<br>
<br>
<blockquote type="cite">I'm missing GERP p-value but I can't find
it inside
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1ConservationScore.html">http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1ConservationScore.html</a>
<br>
<br>
It's ok. I'll take a look further.
<br>
<br>
Thanks.
<br>
<br>
Best regards,
<br>
Guillermo.
<br>
<br>
<blockquote type="cite">Hi Guillermo,
<br>
<br>
I'm not exactly sure what question you are asking; the
Conservation.pm
<br>
plugin by default fetches GERP conservation scores, but the
plugin's
<br>
configuration allows you to specify a different method e.g.:
<br>
<br>
--plugin Conservation,[alt_method]
<br>
<br>
I'm not familiar with this area of the API - you should
consult the
<br>
Compara
<br>
documentation:
<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/compara/index.html">http://www.ensembl.org/info/docs/compara/index.html</a>
<br>
<br>
Regards
<br>
<br>
Will
<br>
<br>
<br>
On 28 May 2013 17:04, Guillermo Marco Puche <
<br>
<a class="moz-txt-link-abbreviated" href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a>> wrote:
<br>
<br>
<blockquote type="cite"> Hello,
<br>
<br>
I'm using Conservation score plugin from VEP repository. But
I've a
<br>
doubt
<br>
since long time ago I used GERP method (which I believe is
now
<br>
deprecated).
<br>
<br>
I'm confused, so now Conservation score equals GERP?
(*Genomic
<br>
Evolutionary Rate Profiling* score is the estimation of the
conservation
<br>
for a position in the evolutionary scale through multiple
alignments)
<br>
<br>
Thank you :)
<br>
<br>
Best regards,
<br>
Guillermo.
<br>
<br>
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