[ensembl-dev] compara api: paralogous DNAs

[Jin-Rui Xu]

Hi Matthieu,

Thank you very much for your email.

I am wondering in the human self alignment, one genomic region may be
mapped to multiple other regions. These multiple hits also exist in e.g.
human vs mouse genome alignment.
Does ensembl provide all these multiple regions or just the best one? Can
these multiple hits achieved by compara perl API?

Thanks!
Jinrui





On Mon, Mar 11, 2019 at 3:05 PM Matthieu Muffato <muffato at ebi.ac.uk> wrote:

> Dear Jinrui,
>
> We have a human self-alignment, that has been computed with LastZ and
> identifies paralogous regions within the genome. You can find the whole
> alignment on the FTP
> ftp://ftp.ensembl.org/pub/current_maf/ensembl-compara/pairwise_alignments/
> but also query specific regions:
>
> http://rest.ensembl.org/alignment/region/homo_sapiens/17:63997797-64000390:1?species_set=homo_sapiens;content-type=application/json;method=LASTZ_NET
>
> Human is the only species for which we have a self-alignment.
>
> Kind regards,
> Matthieu
>
> On 09/03/2019 03:10, Jin-Rui Xu wrote:
> > Hello,
> >
> > I just started learning the compara API. However, I am still not sure
> > whether it can address my questions. I am wondering if someone could
> > give me some guidance and example scripts. Here is my question: (1) I
> > want to identify all paralogous DNA fragments (not neccessarily genes)
> > in a genome. One genomic regions may have more than one duplicate. (2)
> > Then, I want to find in which of the other species, the two paralogous
> > DNAs have a common ancestor.
> > Alternatively, I can focus on two genomic regions in a genome to test
> > if they are paralogous, and then which species has their common
> > ancestral DNA
> > How could I get this done using compara API (version 95)?
> >
> > Many thanks!
> >
> > Jinrui
>
> --
> Matthieu Muffato, Ph.D.
> Ensembl Compara and TreeFam Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus, Hinxton
> Cambridge, CB10 1SD, United Kingdom
> Room  A3-145
> Phone + 44 (0) 1223 49 4631
> Fax   + 44 (0) 1223 49 4468
>
>
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