[ensembl-dev] apparent and low confidence orthology

[Matthieu Muffato]

It is a boolean: only 0 or 1

Matthieu

On 16/03/15 09:42, Julien Roux wrote:
> Thanks a lot Matthieu for the detailed answer.
> Just one last question: is the "is_tree_compliant" score only 0 or 1, or
> can it take any value between 0 and 1?
> Julien
>
> On 3/13/15 5:38 PM, Matthieu Muffato wrote:
>> Dear Julien
>>
>> API's is_tree_compliant() is the same as BioMart's confidence.
>> It tells you whether the pair of genes should be considered as
>> orthologues when looking at the tree (i.e. is their LCA a speciation
>> node).
>>
>> apparent_ortholog_one2one is now ortholog_one2one with a "low
>> confidence" / is_tree_compliant=0. possible_ortholog have also been
>> merged into the standard orthology categories with the same "low
>> confidence" / is_tree_compliant=0.
>> In your case, I think you should select all the "high confidence" /
>> is_tree_compliant=1.
>>
>> We don't have compute scores per homology, but only for the
>> duplication/dubious nodes. The formula only depends on the
>> distribution of species absence/presence under the two sub-trees,
>> regardless of the annotation of the other internal nodes (above or below)
>>
>> Hope this helps,
>> Matthieu
>>
>> On 13/03/15 07:45, Julien Roux wrote:
>>> Dear mailing list,
>>>
>>> I am wondering how to access information on the homology objects using
>>> the Compara API. In particular I would like to be sure that an orthology
>>> relationships I am looking at are not an "apparent" orthology
>>> relationships (reciprocal gene losses after a duplication event)
>>> A few years ago, this info used to be included in the description()
>>> field (e.g., "apparent_orthology"), but it doesn't seem to be the case
>>> any more.
>>> In the documentation I have seen the function is_tree_compliant(). What
>>> is it giving?
>>> Also in Biomart, you can get an orthology confidence score [0 low, 1
>>> high]. What does it mean and how is it calculated? How do you access it
>>> using the API?
>>>
>>> Last question: is there a score difference between an apparent orthology
>>> following a duplication node or following a dubious duplication node?
>>>
>>> Thnaks for you help
>>> Julien
>>>
>>
>

-- 
Matthieu Muffato, Ph.D.
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-145
Phone + 44 (0) 1223 49 4631
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