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    Dear list,<br>

    I am trying to retrieve, for a given human genomic region, the

    nucleotidic sequence conservation based on the EPO 8-ways genomic

    alignments.<br>

    I successfully managed to extract the genomic alignment of a

    specific human region (see attached script) using help from the

    tutorial

    (<a class="moz-txt-link-abbreviated" href="http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html">www.ensembl.org/info/docs/api/compara/compara_tutorial.html</a>), and

    with the

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    MethodLinkSpeciesSetAdaptor parameters detailed here:

    <a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/genome/compara/analyses.html">http://www.ensembl.org/info/genome/compara/analyses.html</a><br>

    Thanks for that!<br>

    <br>

    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?<br>

    <br>

    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

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    Bio::EnsEMBL::Compara::GenomicAlignBlock objects. What does it

    correspond to?<br>

<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1GenomicAlignBlock.html#aa1480f9cf9068f9102f67e8b586f1cce">http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1GenomicAlignBlock.html#aa1480f9cf9068f9102f67e8b586f1cce</a><br>

    I also found this, but I have no idea if it can be used for genomic

    alignments: <br>

<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1ConservationScore.html">http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1ConservationScore.html</a><br>

    <br>

    Thanks for any tip!<br>

    Best<br>

    Julien<br>

    <br>

    <pre class="moz-signature" cols="72">-- 

Julien Roux

Marie-Curie postdoctoral fellow

Department of Ecology and Evolution, University of Lausanne, Switzerland

<a class="moz-txt-link-freetext" href="http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html">http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html</a>

Tel: +41 78 700 2931

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