[ensembl-dev] Conservation_score = GERP?

[Kathryn Beal]

Hi,
Your module looks to be fine, I can find regions which report more than one score:
eg
20_70485_TCTT/- 20:70485-70488  -       ENSG00000178591 ENST00000382410 Transcript      intron_variant,feature_truncation       -       -       -       -       -       -       Conservation=-0.557,-3.710,0.660,-0.666

To view on the web site:
http://www.ensembl.org/Homo_sapiens/Location/View?db=core;r=20:70485-70488

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:
eg
20_120591_AAGTC/-       20:120591-120595        -       ENSG00000125788 ENST00000542572 Transcript      upstream_gene_variant   -       -       -       -       -       -       Conservation=0.114,0.114;DISTANCE=2680
Here only 2 of the 5 positions have a score and the 36 way eutherian alignment looks like:
http://www.ensembl.org/Homo_sapiens/Location/Compara_Alignments?align=622;db=core;r=20:120591-120595
Homo sapiens         AAGTC
Pongo abelii         AA---
Nomascus leucogenys  AAGTC
Macaca mulatta       AA---
Does that help?
Cheers
Kathryn

Kathryn Beal, PhD
European Bioinformatics Institute  (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK 
Tel. +44 (0)1223 494458
www.ensembl.org

On 3 Jun 2013, at 08:49, Guillermo Marco Puche wrote:

> Hello,
> 
> Thank you very much for all this information. It has been really helpful.
> 
> 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. 
> 
> You can have a look at the code right here: https://github.com/guillermomarco/vep_plugins_71/blob/master/Conservation.pm
> 
> Modified lines from 165 to 180.
> 
> Thank you.
> 
> Best regards,
> Guillermo.
> 
> On 05/29/2013 02:43 PM, Stephen Fitzgerald wrote:
>> Hi Guillermo, 
>> 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. 
>> The diff_score = expected_score - observed_score. 
>> So, the more positive the diff_score is the more resistant to substitutions 
>> 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. 
>> 
>> Hope that helps, 
>> Stephen. 
>> 
>> 
>> On Wed, 29 May 2013, guillermo.marco at sistemasgenomicos.com wrote: 
>> 
>>> I'm missing GERP p-value but I can't find it inside 
>>> http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1ConservationScore.html 
>>> 
>>> It's ok. I'll take a look further. 
>>> 
>>> Thanks. 
>>> 
>>> Best regards, 
>>> Guillermo. 
>>> 
>>>> Hi Guillermo, 
>>>> 
>>>> I'm not exactly sure what question you are asking; the Conservation.pm 
>>>> plugin by default fetches GERP conservation scores, but the plugin's 
>>>> configuration allows you to specify a different method e.g.: 
>>>> 
>>>> --plugin Conservation,[alt_method] 
>>>> 
>>>> I'm not familiar with this area of the API - you should consult the 
>>>> Compara 
>>>> documentation: 
>>>> 
>>>> http://www.ensembl.org/info/docs/compara/index.html 
>>>> 
>>>> Regards 
>>>> 
>>>> Will 
>>>> 
>>>> 
>>>> On 28 May 2013 17:04, Guillermo Marco Puche < 
>>>> guillermo.marco at sistemasgenomicos.com> wrote: 
>>>> 
>>>>>  Hello, 
>>>>> 
>>>>> I'm using Conservation score plugin from VEP repository. But I've a 
>>>>> doubt 
>>>>> since long time ago I used GERP method (which I believe is now 
>>>>> deprecated). 
>>>>> 
>>>>> I'm confused, so now Conservation score equals GERP? (*Genomic 
>>>>> Evolutionary Rate Profiling* score is the estimation of the conservation 
>>>>> for a position in the evolutionary scale through multiple alignments) 
>>>>> 
>>>>> Thank you :) 
>>>>> 
>>>>> Best regards, 
>>>>> Guillermo. 
>>>>> 
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