<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<p>I have tried writing an example UniProt api query [1] to retrieve
Ensembl transcript references in Uniprot/swissprot<br>
</p>
<p> -
<a class="moz-txt-link-freetext" href="https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+insulin&columns=database(Ensembl)&format=tab">https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606+AND+insulin&columns=database(Ensembl)&format=tab</a></p>
<p>Regards,</p>
<p>--mahmut<br>
</p>
<p>[1] <a class="moz-txt-link-freetext" href="https://www.uniprot.org/help/api_queries">https://www.uniprot.org/help/api_queries</a></p>
<div class="moz-cite-prefix">On 10/29/19 4:47 PM, Anja Thormann
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:88FB30C1-85C9-4564-962C-627FBD04B9AB@ebi.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hi Dayana,
<div class=""><br class="">
</div>
<div class="">you could fetch the XML file from uniprot, e.g. <a
href="https://www.uniprot.org/uniprot/Q96MT7.xml" class=""
moz-do-not-send="true">https://www.uniprot.org/uniprot/Q96MT7.xml</a><br
class="">
<br class="">
Then find the <dbReference> tag with type="ensembl"
attribute. The section looks like this:<br class="">
<br class="">
<dbReference type="Ensembl" id="ENST00000295868"><br
class="">
<molecule id="Q96MT7-1"/><br class="">
<property type="protein sequence ID"
value="ENSP00000295868"/><br class="">
<property type="gene ID" value="ENSG00000206530"/><br
class="">
</dbReference></div>
<div class=""><br class="">
</div>
<div class="">A txt version is also available <a
href="https://www.uniprot.org/uniprot/Q96MT7.txt" class=""
moz-do-not-send="true">https://www.uniprot.org/uniprot/Q96MT7.txt</a></div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class="">Anja</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 29 Oct 2019, at 12:38, Dayana Yahalomi <<a
href="mailto:dayana.yahalomi@weizmann.ac.il" class=""
moz-do-not-send="true">dayana.yahalomi@weizmann.ac.il</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="WordSection1" style="page: WordSection1;
caret-color: rgb(0, 0, 0); font-family: Helvetica;
font-size: 12px; font-style: normal; font-variant-caps:
normal; font-weight: normal; letter-spacing: normal;
text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; text-decoration: none;">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><span style="font-size: 11pt; color: rgb(31,
73, 125);" class="" lang="en-IL">Hi Anja,<o:p
class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><span style="font-size: 11pt; color: rgb(31,
73, 125);" class="" lang="en-IL">This is great
thanks for all the explanations and the examples.<o:p
class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><span style="font-size: 11pt; color: rgb(31,
73, 125);" class="" lang="en-IL">Now I understand.<o:p
class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><span style="font-size: 11pt; color: rgb(31,
73, 125);" class="" lang="en-IL">Specifically for
me, and maybe others, I do need to know the isoform
suffix. Is there a way to know/import for each
Ensembl transcript the cross-reference in
Uniprot/swissprot including the isoform suffix?<o:p
class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><span style="font-size: 11pt; color: rgb(31,
73, 125);" class="" lang="en-IL"><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><span style="font-size: 11pt; color: rgb(31,
73, 125);" class="" lang="en-IL">Thanks,<o:p
class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><span style="font-size: 11pt; color: rgb(31,
73, 125);" class="" lang="en-IL">Dayana<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><span style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73, 125);"
class=""><o:p class=""> </o:p></span></div>
<div class="">
<div style="border-style: solid none none;
border-top-width: 1pt; border-top-color: rgb(225,
225, 225); padding: 3pt 0cm 0cm;" class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><b class=""><span
style="font-size: 11pt; font-family: Calibri,
sans-serif;" class="">From:</span></b><span
style="font-size: 11pt; font-family: Calibri,
sans-serif;" class=""><span
class="Apple-converted-space"> </span>Dev <<a
href="mailto:dev-bounces@ensembl.org" class=""
moz-do-not-send="true">dev-bounces@ensembl.org</a>><span
class="Apple-converted-space"> </span><b
class="">On Behalf Of<span
class="Apple-converted-space"> </span></b>Anja
Thormann<br class="">
<b class="">Sent:</b><span
class="Apple-converted-space"> </span>Tuesday,
29 October 2019 14:12<br class="">
<b class="">To:</b><span
class="Apple-converted-space"> </span>Ensembl
developers list <<a
href="mailto:dev@ensembl.org" class=""
moz-do-not-send="true">dev@ensembl.org</a>><br
class="">
<b class="">Subject:</b><span
class="Apple-converted-space"> </span>Re:
[ensembl-dev] output I get for my input file
different when I use the web VEP and command
line VEP<o:p class=""></o:p></span></div>
</div>
</div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class="">Hi Dayana,<o:p class=""></o:p></div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class="">we import our protein
cross-references from UniProt. As part of the
import we do alignments to provide identity
scores. They can be seen on the website, and are
usually 100% or close to.<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class="">There can be two different
Ensembel proteins sequences pointing to the same
swissprot id.<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class="">For example:<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><a
href="https://www.uniprot.org/uniprot/Q96MT7"
style="color: purple; text-decoration:
underline;" class="" moz-do-not-send="true">https://www.uniprot.org/uniprot/Q96MT7</a><o:p
class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class="">You can see that UniProt
associates both isoforms with one gene, but
different proteins. In the source data we see:<o:p
class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class="">DR Ensembl; ENST00000295868;
ENSP00000295868; ENSG00000206530. [Q96MT7-1]<o:p
class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class="">DR Ensembl; ENST00000393845;
ENSP00000377428; ENSG00000206530. [Q96MT7-2]<o:p
class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class="">In Ensembl we see that the
isoform suffix is not imported:<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><a
href="https://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000206530;r=3:113362865-113441610;t=ENST00000295868"
style="color: purple; text-decoration:
underline;" class="" moz-do-not-send="true">https://www.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000206530;r=3:113362865-113441610;t=ENST00000295868</a><o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class="">Please let me know if you have any further
questions.<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><o:p class=""> </o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class="">Best wishes,<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class="">Anja<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><o:p class=""> </o:p></div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><br class="">
<br class="">
<o:p class=""></o:p></div>
<blockquote style="margin-top: 5pt; margin-bottom:
5pt;" class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New
Roman", serif;" class="">On 29 Oct 2019,
at 06:57, Dayana Yahalomi <<a
href="mailto:dayana.yahalomi@weizmann.ac.il"
style="color: purple; text-decoration:
underline;" class="" moz-do-not-send="true">dayana.yahalomi@weizmann.ac.il</a>>
wrote:<o:p class=""></o:p></div>
</div>
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New Roman",
serif;" class=""><o:p class=""> </o:p></div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73,
125);" class="">Hi Anja,</span><o:p
class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73,
125);" class="">Thanks for the response
and the information.</span><o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73,
125);" class="">I am so sorry!!! I just
noticed that the problem is in my script
while parsing the two files.</span><o:p
class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73,
125);" class=""> </span><o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73,
125);" class="">But it was very helpful to
find out that the coordinates are for the
ENSP.. and not swissprot. Thanks again for
this information.</span><o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73,
125);" class=""> </span><o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73,
125);" class="">I hope it is O.K to bother
you with one last question. isn’t the
Ensembel protein supposed to be 100% match
to the swissprot? Can there be two
different Ensembel proteins sequences, two
different ENSP.. id’s (maybe isoforms),
pointing to the same swissprot id?</span><o:p
class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73,
125);" class=""> </span><o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73,
125);" class="">All the best,</span><o:p
class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif; color: rgb(31, 73,
125);" class="">Dayana</span><o:p class=""></o:p></div>
</div>
<div class="">
<div style="border-style: solid none none;
border-top-width: 1pt; border-top-color:
rgb(225, 225, 225); padding: 3pt 0cm 0cm;"
class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family:
"Times New Roman", serif;"
class=""><b class=""><span
style="font-size: 11pt; font-family:
Calibri, sans-serif;" class="">From:</span></b><span
class="apple-converted-space"><span
style="font-size: 11pt; font-family:
Calibri, sans-serif;" class=""> </span></span><span
style="font-size: 11pt; font-family:
Calibri, sans-serif;" class="">Dev
<<a
href="mailto:dev-bounces@ensembl.org"
style="color: purple;
text-decoration: underline;"
class="" moz-do-not-send="true">dev-bounces@ensembl.org</a>><span
class="apple-converted-space"> </span><b
class="">On Behalf Of<span
class="apple-converted-space"> </span></b>Anja
Thormann<br class="">
<b class="">Sent:</b><span
class="apple-converted-space"> </span>Monday,
28 October 2019 16:19<br class="">
<b class="">To:</b><span
class="apple-converted-space"> </span>Ensembl
developers list <<a
href="mailto:dev@ensembl.org"
style="color: purple;
text-decoration: underline;"
class="" moz-do-not-send="true">dev@ensembl.org</a>><br
class="">
<b class="">Subject:</b><span
class="apple-converted-space"> </span>Re:
[ensembl-dev] output I get for my
input file different when I use the
web VEP and command line VEP</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""> <o:p
class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class="">Hi Dayana,<o:p
class=""></o:p></div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""> <o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class="">thank
you for the input file and web tool
command line. I annotated your input file
with both the web tool and command line
VEP option and get for both output files
5519 SWISSPROT annotations if I grep
for SWISSPROT. This is not the most in
depth comparison. Could you please point
me to some examples where you see a
difference between the two annotation
options?<o:p class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""> <o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class="">The
coordinates are always given for the
Ensembl protein (ENSP...) which means you
cannot use the protein position to look up
the position in the SwissProt protein.<o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""> <o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class="">However,
you shouldn’t see any differences between
running with the VEP command line tool or
the web online tool.<o:p class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""> <o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class="">Thanks,<o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class="">Anja<o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family:
"Times New Roman", serif;"
class=""><br class="">
<br class="">
<br class="">
<o:p class=""></o:p></div>
</div>
<blockquote style="margin-top: 5pt;
margin-bottom: 5pt;" class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family:
"Times New Roman", serif;"
class="">On 28 Oct 2019, at 11:18,
Dayana Yahalomi <<a
href="mailto:dayana.yahalomi@weizmann.ac.il"
style="color: purple;
text-decoration: underline;"
class="" moz-do-not-send="true"><span
style="color: purple;" class="">dayana.yahalomi@weizmann.ac.il</span></a>>
wrote:<o:p class=""></o:p></div>
</div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family:
"Times New Roman", serif;"
class=""> <o:p class=""></o:p></div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""><span
style="font-size: 11pt;
font-family: Calibri,
sans-serif; color: rgb(31, 73,
125);" class="">Hi Anja,</span><o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""><span
style="font-size: 11pt;
font-family: Calibri,
sans-serif; color: rgb(31, 73,
125);" class="">This is the
command from the web:</span><o:p
class=""></o:p></div>
</div>
</div>
<div style="border: 1pt solid rgb(204,
204, 204); padding: 0cm;" class="">
<p class="MsoNormal" style="margin:
0cm 0cm 3pt; font-size: 12pt;
font-family: "Times New
Roman", serif;
background-color: rgb(240, 240,
240); background-position: initial
initial; background-repeat: initial
initial;"><span style="font-size:
9.5pt; font-family: "Courier
New"; color: rgb(102, 102,
102);" class="">./vep --af
--appris --biotype --buffer_size
500 --check_existing --distance
5000 --mane --polyphen b --pubmed
--regulatory --sift b --species
homo_sapiens --symbol
--transcript_version --tsl
--uniprot --cache --input_file
[input_data] --output_file
[output_file]</span><o:p class=""></o:p></p>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""><span
style="font-size: 11pt;
font-family: Calibri,
sans-serif; color: rgb(31, 73,
125);" class=""> </span><o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""><span
style="font-size: 11pt;
font-family: Calibri,
sans-serif; color: rgb(31, 73,
125);" class="">Attached is a
vcf file.</span><o:p class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""><span
style="font-size: 11pt;
font-family: Calibri,
sans-serif; color: rgb(31, 73,
125);" class=""> </span><o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""><span
style="font-size: 11pt;
font-family: Calibri,
sans-serif; color: rgb(31, 73,
125);" class="">Thanks,</span><o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""><span
style="font-size: 11pt;
font-family: Calibri,
sans-serif; color: rgb(31, 73,
125);" class="">Dayana</span><o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""><span
style="font-size: 11pt;
font-family: Calibri,
sans-serif; color: rgb(31, 73,
125);" class=""> </span><o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div style="border-style: solid none
none; border-top-width: 1pt;
border-top-color: rgb(225, 225,
225); padding: 3pt 0cm 0cm;"
class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""><b
class=""><span
style="font-size: 11pt;
font-family: Calibri,
sans-serif;" class="">From:</span></b><span
class="apple-converted-space"><span style="font-size: 11pt; font-family:
Calibri, sans-serif;"
class=""> </span></span><span
style="font-size: 11pt;
font-family: Calibri,
sans-serif;" class="">Dev
<<a
href="mailto:dev-bounces@ensembl.org"
style="color: purple;
text-decoration:
underline;" class=""
moz-do-not-send="true"><span
style="color: purple;"
class="">dev-bounces@ensembl.org</span></a>><span
class="apple-converted-space"> </span><b class="">On Behalf Of<span
class="apple-converted-space"> </span></b>Anja
Thormann<br class="">
<b class="">Sent:</b><span
class="apple-converted-space"> </span>Monday,
28 October 2019 11:01<br
class="">
<b class="">To:</b><span
class="apple-converted-space"> </span>Ensembl
developers list <<a
href="mailto:dev@ensembl.org"
style="color: purple;
text-decoration:
underline;" class=""
moz-do-not-send="true"><span
style="color: purple;"
class="">dev@ensembl.org</span></a>><br
class="">
<b class="">Subject:</b><span
class="apple-converted-space"> </span>Re: [ensembl-dev] output I get for
my input file different when
I use the web VEP and
command line VEP</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""> <o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class="">Dear
Dayana,<o:p class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""> <o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class="">could
you please share which options
you are using for the web tool?
You can copy the command line
equivalent from the job details
section. Could you also please
share an example for which you
are seeing different
annotations?<o:p class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""> <o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class="">Thank
you,<o:p class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class="">Anja<o:p
class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""><br
class="">
<br class="">
<br class="">
<br class="">
<o:p class=""></o:p></div>
</div>
</div>
<blockquote style="margin-top: 5pt;
margin-bottom: 5pt;" class="">
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times
New Roman", serif;"
class="">On 28 Oct 2019,
at 07:06, Dayana Yahalomi
<<a
href="mailto:dayana.yahalomi@weizmann.ac.il"
style="color: purple;
text-decoration:
underline;" class=""
moz-do-not-send="true"><span
style="color: purple;"
class="">dayana.yahalomi@weizmann.ac.il</span></a>>
wrote:<o:p class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;"
class=""> <o:p class=""></o:p></div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">Dear Ensembl
dev,</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">I have
installed the
following vep program</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">Versions:</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">
ensembl :
98.e98e194</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">
ensembl-funcgen :
98.36eef94</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">
ensembl-io :
98.052d23b</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">
ensembl-variation :
98.7b96c96</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">
ensembl-vep :
98.2</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class=""> </span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">And When I
run the following
command (offline):</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">./vep
--verbose --species
homo_sapiens
--assembly GRCh38
--offline
--dir_cache=/bio/db/vep98
--input_file ex2.vcf
--format vcf
--output_file
outputfile_uniprot.vep98.2_dayana2.vcf
--vcf --uniprot</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class=""> </span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">I don’t get
the same results as
running the same file
example in your web.</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">I am
interested in the
protein changes and I
look at the SwissProt
flag. I used the
protein name from
SWISSPROT flag and go
to the position
indicated
(Protein_position) and
look if it is correct.</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">In this case
I get fewer protein
changes and 30% are
incorrect comparing to
the web outfile where
I get twice as much
protein changes and
only 10% are incorrect
(this is probably due
to different isoforms
than the one in
Swissprot).</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">Do you know
why I see these
differences in the vcf
outfile?</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class=""> </span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">Thanks in
advance,</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class="">Dayana</span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div class="">
<div style="margin: 0cm
0cm 0.0001pt; font-size:
12pt; font-family:
"Times New
Roman", serif;"
class=""><span
style="font-size:
11pt; font-family:
Calibri, sans-serif;"
class=""> </span><o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times
New Roman", serif;"
class=""><span
style="font-size: 9pt;
font-family: Helvetica,
sans-serif;" class="">_______________________________________________<br
class="">
Dev mailing list </span><a
href="mailto:Dev@ensembl.org" style="color: purple; text-decoration:
underline;" class=""
moz-do-not-send="true"><span
style="font-size: 9pt;
font-family:
Helvetica, sans-serif;
color: rgb(149, 79,
114);" class="">Dev@ensembl.org</span></a><span
style="font-size: 9pt;
font-family: Helvetica,
sans-serif;" class=""><br
class="">
Posting guidelines and
subscribe/unsubscribe
info:<span
class="apple-converted-space"> </span></span><a
href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org"
style="color: purple;
text-decoration:
underline;" class=""
moz-do-not-send="true"><span
style="font-size: 9pt;
font-family:
Helvetica, sans-serif;
color: rgb(149, 79,
114);" class="">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</span></a><span
style="font-size: 9pt;
font-family: Helvetica,
sans-serif;" class=""><br
class="">
Ensembl Blog:<span
class="apple-converted-space"> </span></span><a
href="http://www.ensembl.info/" style="color: purple; text-decoration:
underline;" class=""
moz-do-not-send="true"><span
style="font-size: 9pt;
font-family:
Helvetica, sans-serif;
color: rgb(149, 79,
114);" class="">http://www.ensembl.info/</span></a><o:p
class=""></o:p></div>
</div>
</div>
</div>
</blockquote>
</div>
<div class="">
<div class="">
<div style="margin: 0cm 0cm
0.0001pt; font-size: 12pt;
font-family: "Times New
Roman", serif;" class=""> <o:p
class=""></o:p></div>
</div>
</div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family:
"Times New Roman", serif;"
class=""><ex2m.vcf><span
style="font-size: 9pt;
font-family: Helvetica,
sans-serif;" class="">_______________________________________________<br
class="">
Dev mailing list </span><a
href="mailto:Dev@ensembl.org"
style="color: purple;
text-decoration: underline;"
class="" moz-do-not-send="true"><span
style="font-size: 9pt;
font-family: Helvetica,
sans-serif; color: purple;"
class="">Dev@ensembl.org</span></a><span
style="font-size: 9pt;
font-family: Helvetica,
sans-serif;" class=""><br class="">
Posting guidelines and
subscribe/unsubscribe info:<span
class="apple-converted-space"> </span></span><a
href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org"
style="color: purple;
text-decoration: underline;"
class="" moz-do-not-send="true"><span
style="font-size: 9pt;
font-family: Helvetica,
sans-serif; color: purple;"
class="">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</span></a><span
style="font-size: 9pt;
font-family: Helvetica,
sans-serif;" class=""><br class="">
Ensembl Blog:<span
class="apple-converted-space"> </span></span><a
href="http://www.ensembl.info/"
style="color: purple;
text-decoration: underline;"
class="" moz-do-not-send="true"><span
style="font-size: 9pt;
font-family: Helvetica,
sans-serif; color: purple;"
class="">http://www.ensembl.info/</span></a><o:p
class=""></o:p></div>
</div>
</div>
</blockquote>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt;
font-size: 12pt; font-family: "Times
New Roman", serif;" class=""> <o:p
class=""></o:p></div>
</div>
</div>
<div style="margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: "Times New
Roman", serif;" class=""><span
style="font-size: 9pt; font-family:
Helvetica, sans-serif;" class="">_______________________________________________<br
class="">
Dev mailing list </span><a
href="mailto:Dev@ensembl.org" style="color:
purple; text-decoration: underline;"
class="" moz-do-not-send="true"><span
style="font-size: 9pt; font-family:
Helvetica, sans-serif; color: purple;"
class="">Dev@ensembl.org</span></a><span
style="font-size: 9pt; font-family:
Helvetica, sans-serif;" class=""><br
class="">
Posting guidelines and subscribe/unsubscribe
info:<span class="apple-converted-space"> </span></span><a
href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org"
style="color: purple; text-decoration:
underline;" class="" moz-do-not-send="true"><span
style="font-size: 9pt; font-family:
Helvetica, sans-serif; color: purple;"
class="">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</span></a><span
style="font-size: 9pt; font-family:
Helvetica, sans-serif;" class=""><br
class="">
Ensembl Blog:<span
class="apple-converted-space"> </span></span><a
href="http://www.ensembl.info/"
style="color: purple; text-decoration:
underline;" class="" moz-do-not-send="true"><span
style="font-size: 9pt; font-family:
Helvetica, sans-serif; color: purple;"
class="">http://www.ensembl.info/</span></a><o:p
class=""></o:p></div>
</div>
</blockquote>
</div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt;
font-family: "Times New Roman", serif;"
class=""><o:p class=""> </o:p></div>
</div>
</div>
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
text-decoration: none; float: none; display: inline
!important;" class="">_______________________________________________</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
text-decoration: none; float: none; display: inline
!important;" class="">Dev mailing list <a
href="mailto:Dev@ensembl.org" class=""
moz-do-not-send="true">Dev@ensembl.org</a></span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
text-decoration: none; float: none; display: inline
!important;" class="">Posting guidelines and
subscribe/unsubscribe info: <a
href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org"
class="" moz-do-not-send="true">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a></span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
text-decoration: none; float: none; display: inline
!important;" class="">Ensembl Blog: <a
href="http://www.ensembl.info/" class=""
moz-do-not-send="true">http://www.ensembl.info/</a></span></div>
</blockquote>
</div>
<br class="">
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
</body>
</html>