[ensembl-dev] COMPARA get orthologous genes

[Matthieu Muffato]

Hi Nathalie,

It seems that you are using the genomic alignments to map the human 
genes to the mouse genes. There is another way of achieving the same 
goal by using the homology data (based on protein alignments and 
phylogenetic trees).
You would have to create a GeneMember object from the human gene stable 
ID, and then call the fetch_all_by_Member_paired_species() to get the 
homology objects and the mouse genes

There is an example in the workshop materials: 
http://www.ebi.ac.uk/~muffato/workshops/2013_06_Marseille/solutions/homology3.html
The exercise was about getting the human orthologues of two mouse genes, 
and the pairwise alignments

Hope this helps,
Matthieu

On 23/07/13 12:36, nconte at ebi.ac.uk wrote:
> thanks at the moment I am fetching them going throught
> geneHUMAN--->sliceHUMAN---slice(MOUSE)--->geneMOUSE which is not
> straightforward but I had the code ready. DO you have a piece of working
> code I could try quickly?
> thanks
> Nathallie
>
>> Hi Nathalie
>>
>> You may also consider using fetch_all_by_Member_paired_species() to
>> directly get the homologues in a given species
>>
>> Best,
>> Matthieu
>>
>> On 19/07/13 17:48, Denise Carvalho-Silva wrote:
>>> Hi Nathalie,
>>>
>>> The object adaptor is HomologyAdaptor, which has a fetching method
>>> called
>>> fetch_all_by_Member()
>>>
>>> First you will fetch the GeneMember and then you can get the homologies
>>> where the member is involved.
>>>
>>> More information and examples can be found below:
>>>
>>> http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html
>>>
>>> (under ´Homology Objects´)
>>>
>>> Hope it helps.
>>>
>>> Cheers,
>>> Denise
>>>
>>>> Hi, I have a human ensembl gene object and want to fetch the mouse
>>>> orthologous gene, what is the best method for this please?
>>>> thanks
>>>> Nathalie
>>
>
>


-- 
Matthieu Muffato, Ph.D.
Ensembl Developer - Comparative Genomics
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom