[ensembl-dev] get conservation of a region based on multi-species genomic alignment

[Julien Roux]

Dear list,
I am trying to retrieve, for a given human genomic region, the 
nucleotidic sequence conservation based on the EPO 8-ways genomic 
alignments.
I successfully managed to extract the genomic alignment of a specific 
human region (see attached script) using help from the tutorial 
(www.ensembl.org/info/docs/api/compara/compara_tutorial.html), and with 
the MethodLinkSpeciesSetAdaptor parameters detailed here: 
http://www.ensembl.org/info/genome/compara/analyses.html
Thanks for that!

Now, I would like a conservation score for this region. A sensible score 
could for example be the % of the human nucleotides in this region 
showing a perfect conservation in the 8 species. Or it could be the 
average across all nucleotides in this region of the number of species 
showing the same nucleotide than human. Do you have suggestions, based 
on your experience on which measure to consider?

And before implementing this manually, I would like to be sure that 
something similar is not already implemented or easy to extract from the 
API? For example I've seen a score() function for 
Bio::EnsEMBL::Compara::GenomicAlignBlock objects. What does it 
correspond to?
http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1GenomicAlignBlock.html#aa1480f9cf9068f9102f67e8b586f1cce
I also found this, but I have no idea if it can be used for genomic 
alignments:
http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1ConservationScore.html

Thanks for any tip!
Best
Julien

-- 
Julien Roux
Marie-Curie postdoctoral fellow
Department of Ecology and Evolution, University of Lausanne, Switzerland
http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html
Tel: +41 78 700 2931

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