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

[Tang, Haiming]

HI, Stephen

I followed your instructions and got the bed file.

Column 4 appears to list the species for which that base is the same as in
human, since it looks like Hsap is in every line.  The number in square
brackets [] is just the number of species listed.

But the file doesn’t seem to give the age of the base.

For example: How to interpret Ggor-Hsap-Hsap-Pabe[4] in

"chrY 57107125 57107126 Ggor-Hsap-Hsap-Pabe[4] 120 30,30,255"?

Are Ggor and Hsap ancestral species?

Or Age of base is stored at somewhere else?

Thanks

Haiming
On Fri, Sep 26, 2014 at 2:47 AM, Stephen Fitzgerald <stephenf at ebi.ac.uk>
wrote:

> 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
>>
>>
>>
>>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140926/f78441d7/attachment.html>