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<body><div><br></div><div>Hi Reece</div><div><br></div><blockquote style="margin: 0 0 0.80ex; border-left: #0000FF 2px solid; padding-left: 1ex"><div dir="ltr"><div class="gmail_extra">On Tue, Jun 4, 2013 at 6:41 AM, Thibaut Hourlier <span dir="ltr"><<a href="mailto:th3@sanger.ac.uk" target="_blank">th3@sanger.ac.uk</a>></span> wrote:<br><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div>Just to add to RIshi's answer; only the sequences from RefSeq which align the genome of interest are stored in the otherfeatures database</div>
</blockquote></div><div class="gmail_extra"><br></div>Do you have details about how refseq data are loaded?</div></div></blockquote><div><br></div><div>We use the web front end to download the RefSeq EST and selected cDNA data for a particular species. Once these are downloaded the alignments are run and the sequences that do align will be present in the Ensembl database.</div><div><br></div><div>Here is the procedure.</div><div><br></div><div>EST sequences<br>Go to the NCBI website at http://www.ncbi.nlm.nih.gov <br>In the search bar, select 'EST' as the database and specify the scientific name of your species as the organism query term. eg. "Gallus gallus"[Organism]<br>Under the 'Send To' menu, choose File/FASTA/Default Ordering and save the generated file <br></div><div><br></div><div>cDNA sequences<br><br>Go to the NCBI website at http://www.ncbi.nlm.nih.gov <br>In the search bar, select 'Nucleotide' as the database and specify the scientific name of your species as the organism query term. eg. "Gallus gallus"[Organism]<br>Under the search box at the top of the page click on the 'Limits' link <br>In the 'Exclude' section tick the boxes STSs,working draft,EPA and Patents <br>In the 'Molecule' section select mRNA <br>Click Search <br>Under the 'Send To' menu, choose File/FASTA/Default Ordering and save the generated file <br></div><div><br></div><div>Regards</div><div><br></div><div>Rishi</div><div><br></div><br><br><div id="M2Signature"><div>-- </div><div>Using Opera's mail client: <a href="http://www.opera.com/mail/">http://www.opera.com/mail/</a></div></div></body></html>