<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000066">
<div class="moz-cite-prefix">Hello Kathryn,<br>
<br>
Indeed this does help a lot. Now I'm sure that the modification I
did to the original conservation plugin is working correctly.<br>
<br>
Thank you very much !<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 06/03/2013 12:46 PM, Kathryn Beal wrote:<br>
</div>
<blockquote
cite="mid:33D53337-19D2-469D-8CCA-F105CF015E6D@ebi.ac.uk"
type="cite">
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true" 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
moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true" 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 moz-do-not-send="true"
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 moz-do-not-send="true"
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>
_______________________________________________ <br>
Dev mailing list <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
<br>
Posting guidelines and subscribe/unsubscribe info: <br>
<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
<br>
Ensembl Blog: <a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.ensembl.info/">http://www.ensembl.info/</a>
<br>
<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</body>
</html>