[ensembl-dev] (B)LASTZ alignments in Ensembl Compara

Javier Herrero jherrero at ebi.ac.uk
Wed Feb 6 15:15:38 GMT 2013


Hi Mick

This is correct. The netting step identifies the "best-in-genome" 
alignment. Usually, either human or mouse are the genome of reference 
for this. In other words, the same pig locus can be aligned to two 
regions in human but a given locus (bp actually) can only be aligned to 
one region in pig.

I hope this helps

Javier

On 06/02/13 14:49, WATSON Mick wrote:
> Hi
>
> I'm trying to get to grips with (B)LASTZ alignments in ensembl-compara.
>
> Am I correct to assume that multiple hits are not handled?  i.e. if a region in human has been duplicated in pig, then only one of those relationships will be stored?
>
> Thanks
> Mick
>
>

-- 
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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