[ensembl-dev] MCoffee score ?

Sébastien Moretti sebastien.moretti at unil.ch
Tue Feb 15 14:00:07 GMT 2011


I thought it should be easy to retrieve MCoffee scores from the 
protein_tree_member_score table but it is not.

I cannot find how to link protein_tree_member and 
protein_tree_member_score tables.
The first table is the one with gene tree family identifiers and protein 
The second is the one with MCoffee score.

Similar field names do not seem to be related between both tables.

For example
     SELECT s.cigar_line
     FROM protein_tree_member m, protein_tree_member_score s
     WHERE m.root_id=688 AND s.member_id=m.member_id;
returns nothing.

Have I misunderstood something ?
Should I join these tables with a third one ?


> Could be useful to get this information in the Gene Tree (alignment) pages.
> Will wait for a support in the API but will also try to get it from the
> database directly.
> Thanks
> Sébastien
>> Hi Sébastien
>> I am afraid there is no support in the compara API to retrieve the
>> MCoffee
>> scores at the moment.
>> We will add this to our todo list.
>> Javier
>> On Monday 24 Jan 2011 15:33:05 Sébastien Moretti wrote:
>>> Hi
>>> which method of the compara API should I use to retrieve MCoffee scores
>>> for a gene tree family alignment ?
>>> MCoffee scores seem to be stored in the protein_tree_member_score MySQL
>>> table now. But I cannot find the Perl method to access it.
>>> Regards

Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079

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