[ensembl-dev] Ensembl Release 60 - summary of declarations of intentions

[Javier Herrero]

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

-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK