[ensembl-dev] ncRNA gene trees

[Julien Roux]

Thank you very much for your answers,

NCTree is indeed working, although some of the methods described in the 
NCTree Adaptor do not actually work for ncRNAs (for example 
"fetch_by_Member_root_id")

Another observation is that quite a lot of the NCTrees fail to load 
using the API. This is also the case using the Gene Tree view of the 
Ensembl website...
For example look at:
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000222692
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000215960

What do you think is happening?
Best,
Julien

Le 26.11.10 09:41, Albert Vilella a écrit :
> Substituting "ProteinTree" for "NCTree" in the adaptor should just work.
>
> On Fri, 2010-11-26 at 08:54 +0100, Julien Roux wrote:
>> Dear Ensembl team
>>
>> Is there a way to access the ncRNA gene trees via the Ensembl perl API?
>> (for example miRNA trees like this one:
>> http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?db=core;g=ENSG00000199024;r=20:3898141-3898218;t=ENST00000362154)
>> After some tries, it seems that the usual methods working for protein
>> trees do not work for ncRNA trees...
>>
>> Thanks for any tip
>> Julien
>>
>
>
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-- 
Julien Roux, PhD
http://www.unil.ch/dee/page38327.html
Keller group, Department of Ecology and Evolution
Biophore, University of Lausanne, 1015 Lausanne, Switzerland
tel: +41 21 692 4221    fax: +41 21 692 4165