[ensembl-dev] problem loading ncRNA trees

[Julien Roux]

Dear Ensembl list,
(I had no answer on my previous mail, so I am reposting this)

I noticed that quite a lot of the NCTrees fail to load using the API and 
the website (Gene Tree view).
For example:
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000222692
http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000215960
Is there a way to fix/bypass this?
Thanks a lot
Julien

Le 29.11.10 09:26, Julien Roux a écrit :
> 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
>>>
>>
>>
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
>
>

-- 
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