[ensembl-dev] apparent and low confidence orthology

Matthieu Muffato muffato at ebi.ac.uk
Fri Mar 13 16:38:30 GMT 2015


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
Fax   + 44 (0) 1223 49 4468




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