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Hi Joshua,<br>
<br>
Exons and other features tend to be stored on toplevel sequences,
which are generally chromosomes.<br>
Dna sequence however is stored on the contig level.<br>
The assembly table contains information to map a contig sequence to
a chromosome.<br>
<br>
Retrieving dna sequence directly from the mysql schema is tricky in
the best of case.<br>
This is why we recommend using Biomart, the perl API
(<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/index.html">http://www.ensembl.org/info/docs/api/index.html</a>) or REST queries
(<a class="moz-txt-link-freetext" href="http://rest.ensembl.org">http://rest.ensembl.org</a>) for this type of use.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 24/09/2014 22:53, Joshua Bradley
wrote:<br>
</div>
<blockquote
cite="mid:20140924215403.7BFDA134476_4233D7BB@hx-mx2.ebi.ac.uk"
type="cite">
<div dir="ltr">
<div>
<div style="font-family:arial,sans-serif;font-size:13px">I am
using the the latest release of the human genome,
homo_sapiens_core_76_38.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">I am
trying to map exons to their corresponding dna sequence. I'm
running a local instance of the sql tables to make things
faster. My approach was to take the seq_region_id in the
exon table and use that to find the sequence in the dna
table. . The <a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/core/core_schema.html"
target="_blank">schema</a> online seems to suggest that I
can use the seq_region_id to do this but I am not getting
any results back from my sql queries.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">I've
verified what the schema says, that the seq_region table has
a 1-1 mapping to the dna table by comparing counts between
the two with the following queries.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">SELECT
COUNT(*) FROM seq_region INNER JOIN dna ON
seq_region.seq_region_id=dna.seq_region_id;<br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<span style="font-family:arial,sans-serif;font-size:13px">SELECT
COUNT(*) FROM dna;</span>
<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">This
was to be expected, however when I try to do a join between
the exon table and dna table, I get a count of 0</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">SELECT
COUNT(*) FROM exon INNER JOIN dna ON
exon.seq_region_id=dna.seq_region_id;<br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br>
</div>
<div style="font-family:arial,sans-serif;font-size:13px">which
tells me the seq_region_id is not a 1-1 mapping. I am able
to use <a moz-do-not-send="true"
href="http://www.ensembl.org/biomart/martview/96b01e4e2043c838fc28f0969c5914a6?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.sequences.ensembl_gene_id%7Chsapiens_gene_ensembl.default.sequences.ensembl_transcript_id%7Chsapiens_gene_ensembl.default.sequences.gene_exon%7Chsapiens_gene_ensembl.default.sequences.ensembl_exon_id&FILTERS=hsapiens_gene_ensembl.default.filters.source.%22ensembl%22&VISIBLEPANEL=resultspanel"
target="_blank">biomart</a> (this is a sample query) to
get the exon-to-sequence mapping but I would like a more
automated approach. Can someone explain how biomart is able
to do it? It's possible I am interpreting the schema wrong.
How does seq_region_id in the exon table get mapped to
seq_region_id in the dna table? I appreciate any help.</div>
</div>
<div><br>
</div>
<br clear="all">
<div>Josh Bradley<br>
Graduate Student<br>
University of Maryland - College Park<br>
</div>
</div>
<br>
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