[ensembl-dev] Ancestral alleles information

Wed Aug 7 19:13:59 BST 2024

Hi Murillo,

It's fortunate that you are interested in the marmoset, given that this 
is one of the primate genomes that is already included in comparative 
genomics processing.

We do not currently update Mammals or Primates EPO in every Ensembl 
release. However, as and when the Mammals and Primates EPO are next 
updated, we will endeavour to include the marmoset. If the Primates EPO 
is updated first, ancestral sequences would typically be generated for 
this species as part of our production process. If the Mammals EPO is 
updated first, you would then be able to extract the marmoset's 
ancestral sequence from the Mammals EPO using a command such as the 
following:

/path/to/ensembl-compara/scripts/ancestral_sequences/get_ancestral_sequence.pl 
\
--reg_conf /path/to/ensembl_registry.conf \
--alignment_db Multi \
--ancestral_db ancestral_curr \
--species callithrix_jacchus \
--alignment_set mammals \
--dir /path/to/output_dir/ \
--step 20000000

...where 'ensembl_registry.conf' is an Ensembl registry file, and 
'Multi' and 'ancestral_curr' are the registry aliases of the 
ensembl_compara and ensembl_ancestral databases, respectively.

I hope this is of some help.

Regards,

Thomas Walsh.

On 2024-08-05 17:34, Murillo Rodrigues wrote:

> Hi Thomas,
> 
> Thanks for the detailed response!
> 
> Yes, I was interested in ancestral alleles calls for marmosets. Good to 
> hear that they might be included in an upcoming release.
> 
> Thank you,
> 
> Murillo
> 
> From: Thomas Walsh <twalsh at ebi.ac.uk>
> Date: Friday, August 2, 2024 at 6:13 AM
> To: Ensembl developers list <dev at ensembl.org>
> Cc: Murillo Rodrigues <rodrigmu at ohsu.edu>
> Subject: [EXTERNAL] Re: [ensembl-dev] Ancestral alleles information
> 
> Hi Murillo,
> 
> Thanks for getting in touch and for your interest in the ancestral 
> alleles data.
> 
> I'll try to address each of your questions in turn.
> 
>> How does Ensembl decide which species to call ancestral alleles for?
> 
> My understanding is that the original work on this was done as part of 
> the 1000 Genomes Project, with the 6-Primates EPO being used to 
> generate ancestral sequences, from which the ancestral alleles of human 
> variants were then inferred. If you haven't seen it already, 
> supplementary section 8.3 of the 1000 Genomes paper ( 
> https://doi.org/10.1038/nature15393 [4] ) provides some more detail.
> 
> The Primates EPO has expanded somewhat since then, and ancestral 
> sequences have continued to be available for the Primates EPO species, 
> with ancestral alleles being extracted from these.
> 
> Currently, high-coverage primate genome assemblies that are included in 
> comparative analyses are generally included in the Primates EPO, and 
> included in turn in the set of species with ancestral sequences.
> 
>> Can we request new species be added?
> 
> In general, there's no harm in asking. It may or may not be possible to 
> facilitate such a request, but letting us know here or by contacting 
> Ensembl helpdesk (helpdesk at ensembl.org) will at least help us get a 
> sense of which species users are interested in.
> 
> In this particular case, it depends on the species you are interested 
> in and on our capacity to add it. We are currently very constrained in 
> terms of which species we can add to the Primates EPO, but there are a 
> couple of species -- Marmoset (Callithrix jacchus) and Olive baboon 
> (Papio anubis) -- which might be feasible to include in an upcoming 
> release, as they are already involved in some comparative analyses but 
> not currently in the Primates or Mammals EPO. Would you be interested 
> in the ancestral sequences of either of these two species?
> 
>> Can I run the ancestral allele pipeline for my own species/EPO 
>> alignment of choice?
> 
> There's no harm in trying. Results may vary depending on the species 
> and EPO alignment, and on the phylogenetic context of the species 
> within the EPO species tree. Intuitively, there would likely be a 
> greater number of high-confidence ancestral allele calls for a species 
> nestled among closely related or slowly evolving species, where the 
> sister and ancestral sequences are more likely to be in agreement with 
> each other.
> 
> Regards,
> 
> Thomas Walsh.
> 
> On 2024-07-30 02:01, Murillo Rodrigues wrote:
> 
>> Hi,
>> 
>> I noticed that Ensembl publishes ancestral alleles for a few species, 
>> e.g. https://ftp.ensembl.org/pub/release-112/fasta/ancestral_alleles/ 
>> [1]
>> 
>> These are calculated based on EPO alignments that are built for 
>> subsets of species.
>> 
>> How does Ensembl decide which species to call ancestral alleles for? 
>> Can we request new species be added? Can I run the ancestral allele 
>> pipeline for my own species/EPO alignment of choice?
>> 
>> Thank your for the help!
>> 
>> Murillo
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: 
>> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org [2]
>> Ensembl Blog: http://www.ensembl.info/ [3]
> 
> --
> 
> Thomas Walsh
> 
> Senior Bioinformatician, Ensembl Compara
> 
> European Bioinformatics Institute (EMBL-EBI)
> 
> Wellcome Genome Campus
> 
> Hinxton
> 
> Cambridge CB10 1SD
> 
> United Kingdom
> 
> Email: twalsh at ebi.ac.uk

-- 

Thomas Walsh

Senior Bioinformatician, Ensembl Compara

European Bioinformatics Institute (EMBL-EBI)

Wellcome Genome Campus

Hinxton

Cambridge CB10 1SD

United Kingdom

Email: twalsh at ebi.ac.uk

Links:
------
[1] 
https://urldefense.com/v3/__https:/ftp.ensembl.org/pub/release-112/fasta/ancestral_alleles/__;!!Mi0JBg!J8tEMTvdpLfiqOFUA4UkVX3qOwVCd2I_SNfsLKHbMswIb_UZ8k5ZLuI19afw0WNLzbIqxc56AIeCxjdt$
[2] 
https://urldefense.com/v3/__https:/lists.ensembl.org/mailman/listinfo/dev_ensembl.org__;!!Mi0JBg!J8tEMTvdpLfiqOFUA4UkVX3qOwVCd2I_SNfsLKHbMswIb_UZ8k5ZLuI19afw0WNLzbIqxc56ANsn20bR$
[3] 
https://urldefense.com/v3/__http:/www.ensembl.info/__;!!Mi0JBg!J8tEMTvdpLfiqOFUA4UkVX3qOwVCd2I_SNfsLKHbMswIb_UZ8k5ZLuI19afw0WNLzbIqxc56ALb_irxS$
[4] 
https://urldefense.com/v3/__https:/doi.org/10.1038/nature15393__;!!Mi0JBg!J8tEMTvdpLfiqOFUA4UkVX3qOwVCd2I_SNfsLKHbMswIb_UZ8k5ZLuI19afw0WNLzbIqxc56ABaR05fb$
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