[ensembl-dev] Conservation_score = GERP?

[Guillermo Marco Puche]

Hello Kathryn,

Indeed this does help a lot. Now I'm sure that the modification I did to 
the original conservation plugin is working correctly.

Thank you very much !

Best regards,
Guillermo.

On 06/03/2013 12:46 PM, Kathryn Beal wrote:
> 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 sapiensAAGTC
> Pongo abeliiAA---
> Nomascus leucogenysAAGTC
> Macaca mulattaAA---
> 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 <http://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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>>>>>>
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