[ensembl-dev] Translating ranges quickly using multiple species alignment files ( *.emf )?

Javier Herrero jherrero at ebi.ac.uk
Wed Feb 1 13:19:43 GMT 2012


Hi Robert

We have been working on such a tool, although the input was not the EMF 
files.

Mapping is a complex problem where several solutions are possible and 
the ideal one depends on the application. Typically you will want to map 
segments from one species to the other. The mapping can be very strict 
(no gaps in the alignment for the mapped feature) to very flexible, 
allowing partial matches, etc.

Anyway, let us know if you would be interested in using a mapping tool, 
even if it doesn't use the EMF files.

Kind regards

Javier

On 30/01/12 22:32, Robert Hubley wrote:
> Is there a tool or set of tools to quickly translate a large set of
> coordinates from one genome to another using the multiple species
> alignment format ( *.emf ) as the translation reference?  I want to
> translate a large set of ranges from the Boreoeutherian ancestor to the
> modern human.
>
> Thanks,
>
> -Robert
>
>
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-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK





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