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<div class="moz-cite-prefix">On 21/01/2014 15:05, Greg Slodkowicz
wrote:<br>
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<div>Hi Fiona, </div>
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<div>We do have GTF files for our gene annotations. You
can see a table of all our download files here:</div>
<div><a moz-do-not-send="true"
href="http://www.ensembl.org/info/data/ftp/index.html"
target="_blank">http://www.ensembl.org/info/data/ftp/index.html</a></div>
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<div>Thanks for getting back to me. I've previously
downloaded the GTF file under "Gene sets" but it seems
that it contained coordinates of genes, exons and CDS but
not other functional features such as domains, secondary
structure predictions etc.. Is this the file you're
referring to?</div>
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Hi Greg,<br>
<br>
Apologies, I am not completely clear on what information you would
like to access. The nature paper focuses on conserved regions and
potential gene regulatory sequences, so I will address how to find
that information in Ensembl:<br>
<br>
The Perl API allows programmatic access to conserved and potentially
functional regions of the genome. <br>
<br>
Installation instructions are here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/api_installation.html">http://www.ensembl.org/info/docs/api/api_installation.html</a><br>
<br>
For conserved regions ('constrained elements') the Compara Perl API
is an option- have a look at this tutorial:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html">http://www.ensembl.org/info/docs/api/compara/compara_tutorial.html</a><br>
<br>
If you are looking for hypersensitive sites, transcription binding
sites, and histone modifications, go via the Regulation API:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/funcgen/regulation_tutorial.html">http://www.ensembl.org/info/docs/api/funcgen/regulation_tutorial.html</a><br>
<br>
There is documentation for both our Compara and Regulation resources
here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/genome/compara/index.html">http://www.ensembl.org/info/genome/compara/index.html</a><br>
and<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/genome/funcgen/index.html">http://www.ensembl.org/info/genome/funcgen/index.html</a><br>
<br>
****<br>
If you are looking for protein domains from InterProscan, and
coiled-coil regions from the ncoils program, you can do so through
BioMart or the Perl API.<br>
<br>
BioMart provides an interface for programmers and non-programmers
alike. To learn a bit about how to use the web interface, watch our
quick tutorial:<br>
<br>
BioMart: An Introduction<br>
<a class="moz-txt-link-freetext" href="http://youtu.be/DXPaBdPM2vs">http://youtu.be/DXPaBdPM2vs</a><br>
<br>
You would want to use 'Filters' in the 'PROTEIN DOMAINS' section.<br>
<br>
The API access would be through the Core API.<br>
****<br>
<br>
Let us know if you have any trouble accessing the information you
want, or if you need some further explanation on specific data
types.<br>
<br>
Best wishes,<br>
Giulietta<br>
<br>
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<div> </div>
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<div>What are your features? If they are variation data
you could use our variant effect predictor (VEP) <a
moz-do-not-send="true"
href="http://www.ensembl.org/VEP" target="_blank">http://www.ensembl.org/VEP</a>.</div>
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<div>They're sitewise predictions of evolutionary
constraint, very similar to those from <a
moz-do-not-send="true"
href="http://www.nature.com/nature/journal/v478/n7370/abs/nature10530.html">http://www.nature.com/nature/journal/v478/n7370/abs/nature10530.html</a>.</div>
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<div>Best,</div>
<div>Greg</div>
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-- <br>
<div dir="ltr">Greg Slodkowicz<br>
PhD student, Nick Goldman group<br>
European Bioinformatics Institute (EMBL-EBI)<br>
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