[ensembl-dev] Fetching Age of Base

[Thomas Walsh]

Hi Ben,

Column descriptions for the Age-of-Base bigBed can be found in the 
baseage_autosql.as [1] autosql file.

Col4: "Oldest taxon that possess this base" ... Put another way, this is 
the oldest ancestral sequence sharing the same character state as the 
homologous base in the reference Human genome.
Col5: "Normalised substitution-based age (between 0 -species level- and 
1000 -root of all aligned species-)" ... where the set of aligned 
species are those in the 43 eutherian mammals EPO.

I hope this helps.

All the best,

Tom.

On 2024-04-10 15:07, Benoit Ballester wrote:

> Hi Tom,
> 
> Thanks for the prompt reply.
> 
> What would be the description of col4 and col5 ?
> 
> Col4 Hsap-Mfas-Mmul-Ptro  are the species in which the substitution 
> occurred ?
> Col5 is a score ? age in Mya?
> 
> Thanks
> 
> 19 1581102 1581103 Hsap-Mfas-Mmul-Ptro[4] 319 81,81,255
> 
> 19 1581120 1581121 Hsap-Mfas-Mmul-Ptro[4] 319 81,81,255
> 
> 19 1581138 1581139 Hsap-Mfas-Mmul-Ptro[4] 319 81,81,255
> 
> 19 1581150 1581151 Hsap-Ptro[2] 92 23,23,255
> 
> 19 1581153 1581154 Hsap-Ptro[2] 92 23,23,255
> 
> 19 1581174 1581175 Hsap-Mfas-Mmul-Ptro[4] 319 81,81,255
> 
> 19 1581186 1581187 Hsap-Mfas-Mmul-Ptro[4] 319 81,81,255
> 
> 19 1581189 1581190 Hsap-Mfas-Mmul-Ptro[4] 319 81,81,255
> 
> 19 1581219 1581220 Hsap-Mfas-Mmul-Ptro[4] 319 81,81,255
> 
> 19 1581249 1581250 Hsap-Ptro[2] 92 23,23,255
> 
> 19 1581258 1581259 Hsap-Mfas-Mmul-Ptro[4] 319 81,81,255
> 
> --
> Benoît Ballester, PhD
> INSERM U1090 TAGC
> Aix-Marseille-Université
> Parc Scientifique de Luminy
> 13288 Marseille Cedex 9. France
> 
> (1st)  benoit.ballester at inserm.fr
> (2nd) benoit.ballester at univ-amu.fr
> ReMap: http://remap.univ-amu.fr/
> 
> On 10 Apr 2024, at 15:50, Thomas Walsh <twalsh at ebi.ac.uk> wrote:
> 
> Dear Ben,
> 
> Age-of-Base is not currently stored in Compara databases, but if you 
> have bigBedToBed installed, you can fetch current Age-of-Base data for 
> your region of interest as follows:
> 
> bigBedToBed 
> https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/compara/Hsap_ages_2072_111.bb 
> \
> -chrom=19 -start=1581090 -end=1581269 Hsap_ages_19_1581091_1581269.bed
> 
> The Age-of-Base file is periodically updated, so it may be no harm to 
> keep an eye out for updated versions of the file at: 
> https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/compara/
> 
> All the best,
> 
> Tom Walsh.
> 
> On 2024-04-09 16:21, Benoit Ballester wrote:
> 
> Dear Ensembl,
> 
> I am trying to get the "age of base" as described here :
> https://www.ensembl.org/info/genome/compara/age_of_base.html
> 
> Basically, for a slice like this, I'd like to get those "age".
> $slice = $hsap_slice_adaptor->fetch_by_region( 'toplevel', '19' , 
> '1581091','1581269');
> 
> It has been a while since I last used the ensembl API (prob ~v60), so I 
> wonder if I could get those values from a core slice (which I doubt), 
> most likely from a compara object, but which one ? Is this something 
> stored in the compara db for human, or computed on the fly from a 
> multiple alignment objet ?
> 
> The Doxygen doc is not of much of any help for me I am afraid, as I 
> can't get much info there.
> 
> Any embryo of code to get me on track would be must appreciated.
> 
> I am on version 111 of core and compara.
> 
> Thanks,
> Ben
> 
> --
> Benoît Ballester, PhD
> Inserm U1090, TAGC
> Campus de Luminy
> 13288 Marseille Cedex 9
> France
> +33 4 91 82 87 28
> (1st)  benoit.ballester at inserm.fr
> (2nd) benoit.ballester at univ-amu.fr
> ReMap2022: http://remap.univ-amu.fr/
> _______________________________________________
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> 
> --
> 
> 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://github.com/Ensembl/ensembl-compara/blob/7e5f41ef83e74929ae2c4b444a061051de3f4356/scripts/pipeline/baseage_autosql.as
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