[ensembl-dev] Transcript statistics from ensembl API

[Andy Yates]

Hi Brett,

I believe the website requests the cDNA & peptide sequence and does a length on them both. So you can request the sequence from our /sequence/id endpoint [1].

As for exons you can use the /lookup/id [2] endpoint & the expand=1 parameter to expand the transcript to include all of its exons. However this summary does not contain any information about coding boundaries. I don't believe it is possible to differentiate this easily using the REST API at the moment.

Alternatively the Perl API can do this from a transcript quite easily:

my $exon_count = scalar(@{$transcript->get_Exons()});
my $coding_exon_count = scalar(@{$transcript->get_all_translateable_Exons()});

Hope this helps,

Andy

[1] - http://beta.rest.ensembl.org/documentation/info/sequence_id
[2] - http://beta.rest.ensembl.org/documentation/info/lookup and for BRAF's 1st transcript http://beta.rest.ensembl.org/lookup/id/ENST00000288602.json?expand=1

------------
Andrew Yates - Ensembl Support Coordinator
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
http://www.ensembl.org/

On 8 May 2014, at 16:49, Brett Thomas <bthomas at atgu.mgh.harvard.edu> wrote:

> Hey -- the ensembl browser has the following statistics for each transcript: 
> 
> Exons: 10 Coding exons: 10 Transcript length: 1,577 bps Translation length: 491 residues
> 
> Are they accessible through the ensembl API? (Preferably REST, or perl) 
> 
> Thanks! 
> Brett
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