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Hi Manuel<br>
<br>
Have you seen our API course on EBI Train Online:<br>
<a class="moz-txt-link-freetext" href="http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop">http://www.ebi.ac.uk/training/online/course/ensembl-filmed-api-workshop</a><br>
<br>
The Core section will introduce you to the API itself, and the
Compara module for alignments.<br>
<br>
Hope this helps<br>
<br>
Emily<br>
<br>
<div class="moz-cite-prefix">On 13/01/2014 13:32, Manuel Rodríguez
Pascual wrote:<br>
</div>
<blockquote
cite="mid:CAE_0zefXf2nEfUSTamHpHMp7cJ3WqVzMR4mQF2OuWnHJYXmMug@mail.gmail.com"
type="cite">
<div dir="ltr">
<div style="font-family:arial,sans-serif;font-size:13px">I am
just starting working with <span class=""
style="background-color:rgb(255,255,204)">Ensembl</span> API.
I am not really experienced neither with <span class=""
style="background-color:rgb(255,255,204)">Ensembl</span> or
bioinformatics itself,so I am stuck in a problem that seems to
be easy to solve.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">As a
test and proof of concept, I am interested to retrieve
information of a comparison in phylip format. In particular,
the provided example</div>
<div style="font-family:arial,sans-serif;font-size:13px"><a
moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Gene/Compara_Alignments?align=548&db=core&g=ENSG00000171105&r=19%3A7112266-7294045"
target="_blank">http://www.<span class=""
style="background-color:rgb(255,255,204);color:rgb(34,34,34)">ensembl</span>.org/Homo_sapiens/Gene/Compara_Alignments?align=548&db=core&g=ENSG00000171105&r=19%3A7112266-7294045</a></div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">when
exported into a phylip format, </div>
<div style="font-family:arial,sans-serif;font-size:13px">
<br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><a
moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Export/Output/Location/Alignment?align=548;db=core;g=ENSG00000171105;output=alignment;r=19:7112266-7294045;format=phylip;_format=Text"
target="_blank">http://www.<span class=""
style="background-color:rgb(255,255,204);color:rgb(34,34,34)">ensembl</span>.org/Homo_sapiens/Export/Output/Location/Alignment?align=548;db=core;g=ENSG00000171105;output=alignment;r=19:7112266-7294045;format=phylip;_format=Text</a></div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">I have
however seen that the employment of wget is discouraged and
the <span class="" style="background-color:rgb(255,255,204)">Ensembl</span> API
should be used instead.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">Reading
the available documentation, I fell that I should use the
Compara API Tutorial, </div>
<div style="font-family:arial,sans-serif;font-size:13px">
<a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html"
target="_blank">http://www.<span class=""
style="background-color:rgb(255,255,204);color:rgb(34,34,34)">ensembl</span>.org/info/docs/api/compara/compara_tutorial.html</a><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">but I
don't really understand it or how to apply it to my objective.</div>
<div style="font-family:arial,sans-serif;font-size:13px">
<br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">The
question is, can anyone orient me on how to proceed? <br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">
<br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">Thanks
for your attention,</div>
<div style="font-family:arial,sans-serif;font-size:13px">
<br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">Manuel </div>
<div style="font-family:arial,sans-serif;font-size:13px">
<br clear="all">
<div><br>
</div>
-- <br>
Dr. Manuel Rodríguez-Pascual<br>
skype: manuel.rodriguez.pascual<br>
phone: (+34) 913466173 // (+34) 679925108<br>
<br>
CIEMAT-Moncloa<br>
Edificio 22, desp. 1.25<br>
Avenida Complutense, 40 <br>
28040- MADRID<br>
SPAIN</div>
</div>
<br>
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<pre wrap="">_______________________________________________
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr Emily Pritchard
Ensembl Outreach Officer
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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