[ensembl-dev] compara api: paralogous DNAs

[Matthieu Muffato]

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