[ensembl-dev] Conservation_score = GERP?

[Stephen Fitzgerald]

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.
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>