[ensembl-dev] compara api: paralogous DNAs

[Jin-Rui Xu]

Hi Matthieu,

The script you provided helps a lot!
For a genomic region in human, I need its alignment in another species.
Therefore, I need to know the species names. Here is the short script, but
it returns no names. My question is how to find the species names used by
the compara API? Another question is about the genomic version, I think by
default the perl API uses human genome 38, but how to use 37 with the API?
Many thanks!
Jinrui

use Bio::EnsEMBL::Registry;


my $registry = 'Bio::EnsEMBL::Registry';


$registry->load_all("configuration_file");




my @species_names = @{$registry->get_all_species() };


print "@species_names\n";



On Wed, Mar 20, 2019 at 1:58 PM Matthieu Muffato <muffato at ebi.ac.uk> wrote:

> Hi Jinrui
>
> Have a look back at my first email. There is an example URL to our REST
> API server to get the alignment of a human region
>
> If you want to use the Perl API, you can adapt
> https://github.com/Ensembl/ensembl-presentation/blob/master/API/Compara/exercises/gab1.pl
>
> Regards,
> Matthieu
> On 18/03/2019 16:53, Jin-Rui Xu wrote:
>
> Hi Matthieu,
>
> I am going to use the human self-alignment to detect paralogous genomic
> regions (particularly non coding regions). But I can not find examples of
> API for this purpose. Could you pass me some scripts or examples where I
> can start? Say I have a human genomic coordinate, and want to find its
> paralogous regions and alignments.
> Many thanks.
> Jinrui
>
> On Wed, Mar 13, 2019 at 8:37 AM Matthieu Muffato <muffato at ebi.ac.uk>
> wrote:
>
>> Hi Jinrui
>>
>> In all our pairwise alignments, we refine the LastZ alignment blocks with
>> two steps called "chaining" and "netting" (see
>> http://europepmc.org/articles/PMC4852398 and
>> http://genomewiki.ucsc.edu/index.php/Chains_Nets for more information).
>> What you get in our database is the product of these two steps.
>> The netting phase is done on the reference species only, we don't do
>> bidirectional netting. This means that there is very little overlap /
>> nesting on the reference species (human in the case of the human vs *
>> alignments). Overlap / nesting is allowed on the non-reference species,
>> though. For instance, in the human-mouse alignments, there are 20,000 pairs
>> of blocks that overlap on human, and 1,900,000 pairs of blocks that overlap
>> on mouse.
>>
>> So in this case, yes you can identify human paralogous regions 1) through
>> the self-alignment and 2) through the human-mouse alignment (or any
>> pairwise alignment that involves human) by finding human regions that align
>> to the same region in the other species
>>
>> Hope this helps,
>>
>> Matthieu
>> On 11/03/2019 19:45, Jin-Rui Xu wrote:
>>
>> 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
>>>
>>> --
>> 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
>>
>> --
> 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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