[ensembl-dev] Conservation_score = GERP?

[Guillermo Marco Puche]

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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