[ensembl-dev] How to retrieve "Age of Base" using a Perl API?

[Stephen Fitzgerald]

Hi Haiming,
the compara API is used to retrieve information from the compara database. 
However the "Age of Base" track is generated from a Bigbed binary file, so 
it is not part of the compara database. The Bigbed file is generated from 
a Bed file. I have transferred this Bed file (from release 76) to our ftp 
site. You can retrieve this file using anonymous ftp from here:

ftp ftp.ebi.ac.uk

cd pub/software/ensembl/stephen/BaseAge/

get base_age_76.bed.gz

Hope this helps,
Stephen.


On Thu, 25 Sep 2014, Tang, Haiming wrote:

> 
> DEAR GROUP, MY NAME IS HAIMING TANG. I'M IN DR PAUL THOMAS'S GROUP IN UNIVERSITY OF SOUTHERN CALIFORNIA.
> 
> I'm trying to retrieve "Age of Base" using Perl API.
> 
> As described in "http://www.ensembl.org/info/genome/compara/analyses.html#age_of_base"
> 
> "Age of Base
> 
> From these ancestral sequences, we infer the age of a base, i.e. the timing of the most recent mutation for each
> base of the genome. Each position of the human genome is compared to its immediate inferred ancestor, then its
> ancestor, etc. until a difference is found. The inferred substitution event therefore occurred on a specific
> branch of the tree, which is identified by all the extant species which eventually descended from that branch, as
> illustrated below."
> 
> "Age of base" has close relation with EPO ancestral alignment. But I could find any related method in Compara Perl
> API Documentation or Compara API Tutorial.
> 
> Can anyone show me how to do to retrieve "age of base"?
> 
> Thank you in advance.
> 
> Haiming
> 
> 
>