[ensembl-dev] non-miRNA non-coding orthologues

[Rhoda Kinsella]

Hi Umberto
Our comparative genomics team currently provide trees for short ncRNAs only. This is because we base our ncRNA gene trees on RFAM families and the lincRNAs in ensembl are not currently annotated based on RFAM. This may change in the future. There is some documentation you may find useful on the following links:

http://www.ensembl.org/info/genome/genebuild/ncrna.html

http://www.ensembl.org/info/genome/compara/ncRNA_methods.html

http://www.ensembl.org/info/genome/compara/homology_method.html


As well as miRNA trees we also generate trees for other short ncRNAs (small nucleolar ncRNAs, Small Cajal body-specific RNA, etc...). We don't provide trees for tRNAs for example. Orthologues that are calculated by the comparative genomics team for short ncRNAs will be included in BioMart for each release.

I do hope that helps, but if you have further data questions, please email helpdesk at ensembl.org
Regards
Rhoda


On 9 Sep 2013, at 14:16, umberto.perron at studenti.unito.it wrote:

> Dear all,
> 
> from biomart we are able to obtain all the non-coding
> miRNA orthologues between human and mouse.
> Do data about the other non-coding orthologues like
> lincRNA exist somewhere else?How can we possibly get them?
> Also we'd like to know the procedure you used to obtain
> the non-coding miRNA orthologues present in biomart.
> 
> Cordially
> 
> Umberto Perron
> 
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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton,
Cambridge
CB10 1SD




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