[ensembl-dev] ncRNA gene trees

[Julien Roux]

  Thanks Javier for your answer,
Is it possible to access these trees via the Ensembl perl API?
What would be an efficient way to retrieve only these ncRNA trees? Is it 
possible to know directly if a tree object is made of ncRNA genes?

Thanks for your help
Julien

Le 21.09.10 12:12, Javier Herrero a écrit :
> Hi Julien
>
> Here is an overview of the ncRNA tree pipeline:
>   * ncRNA predictions classified by RFAM ids
>   * Infernal 1.0 alignments
>   * TreeBest MMmerge trees using a combination of NJ and ML on genomic context
> alignment and secondary structure models (raxml ss)
>
> Orthologs are then inferred using the same approach we use for protein-coding
> genes.
>
> Javier
>
> On Tuesday 21 Sep 2010 10:20:37 Julien Roux wrote:
>>    Dear Ensembl team
>>
>>> - Updated build of ncRNA trees
>> Is there a documentation concerning how the trees are built for ncRNA
>> genes (for example miRNAs)?
>>
>> Thanks a lot
>> Julien


-- 
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