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Hi Reece,<br>
<br>
This is correct, we now try to use the refseq transcripts from the
otherfeatures database to infer direct mapping based on overlap with
the ensembl transcript.<br>
Failing that, we use the exonerate alignments as before, but the
first method is given priority.<br>
This will be available for human as of release 71, and we are
planning to do the same for mouse in release 72.<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 04/03/13 23:15, Reece Hart wrote:<br>
</div>
<blockquote
cite="mid:CAKNDN-e8wa=ZAKjNKAEgwjd1E8q7Ai3fSvg7htG+O=mkLbNgnQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div class="gmail_extra">On Mon, Mar 4, 2013 at 5:50 AM, Magali
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div id=":zl">As of release 71, we are also mapping refseq
entries based on<br>
coordinates overlap.<br>
This means that for this particular case, NM_001258395.1
is also mapped<br>
to ENST00000410006.</div>
</blockquote>
</div>
<br>
Do you mean that exact exon structures (i.e., exon start,end
coordinates) will now be used to define equivalence of two
transcripts? What does this portend for RefSeq transcripts
pulled from otherfeatures?</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">We currently precompute the list of
exon-equivalent <ENST,NM> transcript pairs for the
purpose of filtering VEP effects that we can report on RefSeq
transcripts (in otherfeatures). It sounds like we'll be able
to get this equivalence from Ensembl directly with 71. Right?</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra" style="">Thanks,</div>
<div class="gmail_extra" style="">Reece</div>
</div>
<br>
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