<div dir="ltr"><div dir="ltr"><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 24, 2024 at 12:15 PM Benjamin Moore <<a href="mailto:bmoore@ebi.ac.uk" target="_blank">bmoore@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><u></u>
<div>
<p>Hi Allan,</p>
<p>No problem at all- very happy to help. With the GET
sequence/region endpoint, the chromosome number should be entered
as a required parameter instead. From the GET lookup endpoint,
this is the "seq_region_name" key-value pair. In the example you
provided, this is "1", so the URL should look like this instead:</p>
<p><a href="https://rest.ensembl.org/sequence/region/mus_musculus/1:59521583..59522118:1?content-type=text/x-fasta" target="_blank">https://rest.ensembl.org/sequence/region/mus_musculus/1:59521583..59522118:1?content-type=text/x-fasta</a><br>
</p>
<p>Best wishes</p>
<p>Ben<br>
</p>
<div>On 23/04/2024 21:48, Allan Kamau wrote:<br>
</div>
<blockquote type="cite">
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</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Apr 23, 2024 at
10:43 PM Allan Kamau <<a href="mailto:kamauallan@gmail.com" target="_blank">kamauallan@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr"><br>
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<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Apr 23, 2024
at 6:37 PM Benjamin Moore <<a href="mailto:bmoore@ebi.ac.uk" target="_blank">bmoore@ebi.ac.uk</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi
Allan,<br>
<br>
I think the most straightforward way to retreieve the
5'UTR sequences <br>
for a list of Ensembl features (I assume you have a
list of gene IDs, <br>
ENSG...) using the REST API is to use the Lookup
endpoints with the <br>
expand and utr optional parameters to retreieve the
genomic coordinates <br>
of the 5'UTRs of each transcript for your list of
genes:<br>
<br>
<a href="https://rest.ensembl.org/documentation/info/lookup" rel="noreferrer" target="_blank">https://rest.ensembl.org/documentation/info/lookup</a><br>
<br>
Then, you can use the coordinates from the first step
as the input for <br>
the Sequence/region endpoints to retreieve the genomic
sequence of the <br>
5' UTRs:<br>
<br>
<a href="https://rest.ensembl.org/documentation/info/sequence_region" rel="noreferrer" target="_blank">https://rest.ensembl.org/documentation/info/sequence_region</a><br>
<br>
I hope this helps.<br>
<br>
Best wishes<br>
<br>
Ben<br>
<br>
On 23/04/2024 15:30, Allan Kamau wrote:<br>
> Is there a way to obtain 5'UTR sequences given a
list of ensembl ids <br>
> programmatically?<br>
><br>
> I have a list of ensembl ids for which I would
like to obtain the <br>
> 5'UTR region for each one of them
programmatically hopefully via <br>
> ensembl rest using wget, or python
(ensembl-rest).<br>
><br>
> Kindly assist.<br>
><br>
> Thanks.<br>
><br>
> -Allan.<br>
><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe
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> Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
<br>
-- <br>
Dr. Ben Moore (he/him)<br>
Ensembl Outreach Manager<br>
<br>
European Bioinformatics Institute (EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus<br>
Hinxton<br>
Cambridge<br>
CB10 1SD<br>
UK<br>
<br>
<a href="mailto:bmoore@ebi.ac.uk" target="_blank">bmoore@ebi.ac.uk</a><br>
+44 (0)1223 494265<br>
<br>
</blockquote>
<div><br>
</div>
<div>Thank you Ben for your response. I am now stuck in
defining the url for the <a href="https://rest.ensembl.org/sequence/region/" target="_blank">https://rest.ensembl.org/sequence/region</a> resource.</div>
<div><br>
</div>
<div>I am using the ensembl id "ENSMUSG00000041075" in
this example.</div>
<div>The URL below provides the sequence features
the ensembl id object "ENSMUSG00000041075".</div>
<div><br>
</div>
<div><a href="https://rest.ensembl.org/lookup/id/ENSMUSG00000041075?content-type=application/json;expand=1;utr=1" target="_blank">https://rest.ensembl.org/lookup/id/ENSMUSG00000041075?content-type=application/json;expand=1;utr=1</a></div>
<div><br>
</div>
<div>This returns the query below</div>
<div><br>
{
<br>
"ENSMUSG00000041075": {
<br>
"seq_region_name": "1",
<br>
"logic_name":
"ensembl_havana_gene_mus_musculus",
<br>
"end": 59526114,
<br>
"biotype": "protein_coding",
<br>
"version": 9,
<br>
"db_type": "core",
<br>
"object_type": "Gene",
<br>
"strand": 1,
<br>
"start": 59521583,
<br>
"canonical_transcript":
"ENSMUST00000114246.4",
<br>
"Transcript": [
<br>
{
<br>
"biotype": "protein_coding",<br>
"version": 4,<br>
"db_type": "core",<br>
"object_type": "Transcript",<br>
"seq_region_name": "1",<br>
"logic_name":
"ensembl_havana_transcript_mus_musculus",<br>
"end": 59526114,<br>
"Translation": {<br>
"id": "ENSMUSP00000109884",<br>
"length": 572,<br>
"start": 59522119,<br>
"end": 59523837,<br>
"version": 3,<br>
"object_type": "Translation",<br>
"db_type": "core",<br>
"Parent": "ENSMUST00000114246",<br>
"species": "mus_musculus"<br>
},<br>
"assembly_name": "GRCm39",<br>
"Parent": "ENSMUSG00000041075",<br>
"is_canonical": 1,<br>
"display_name": "Fzd7-201",<br>
"Exon": [<br>
{<br>
"species": "mus_musculus",<br>
"version": 4,<br>
"db_type": "core",<br>
"object_type": "Exon",<br>
"assembly_name": "GRCm39",<br>
"id": "ENSMUSE00000698652",<br>
"start": 59521583,<br>
"end": 59526114,<br>
"strand": 1,<br>
"seq_region_name": "1"<br>
}<br>
],<br>
"UTR": [<br>
{<br>
"object_type":
"five_prime_UTR",<br>
"db_type": "core",<br>
"assembly_name": "GRCm39",<br>
"Parent":
"ENSMUST00000114246",<br>
"type": "five_prime_utr",<br>
"species": "mus_musculus",<br>
"seq_region_name": "1",<br>
"strand": 1,<br>
"id": "ENSMUST00000114246",<br>
"source": "ensembl_havana",<br>
"start": 59521583,<br>
"end": 59522118<br>
},<br>
{<br>
"type": "three_prime_utr",<br>
"species": "mus_musculus",<br>
"db_type": "core",<br>
"object_type":
"three_prime_UTR",<br>
"assembly_name": "GRCm39",<br>
"Parent":
"ENSMUST00000114246",<br>
"id": "ENSMUST00000114246",<br>
"source": "ensembl_havana",<br>
"end": 59526114,<br>
"start": 59523838,<br>
"seq_region_name": "1",<br>
"strand": 1<br>
}<br>
],<br>
"species": "mus_musculus",<br>
"strand": 1,<br>
"start": 59521583,<br>
"id": "ENSMUST00000114246",<br>
"source": "ensembl_havana",<br>
"length": 4532<br>
}<br>
],<br>
"id": "ENSMUSG00000041075",<br>
"description": "frizzled class receptor 7
[Source:MGI Symbol;Acc:MGI:108570]",<br>
"source": "ensembl_havana",<br>
"assembly_name": "GRCm39",<br>
"display_name": "Fzd7",<br>
"species": "mus_musculus"<br>
}<br>
}<br>
</div>
<div><br>
</div>
<div>
<div>What would be formulation for the "<a href="https://rest.ensembl.org/sequence/region/" target="_blank">https://rest.ensembl.org/sequence/region/</a>"
for the 5'UTR gene region given above.</div>
<div><br>
</div>
<div>Below is the step where I am stuck.</div>
<div><a href="https://rest.ensembl.org/sequence/region/mus_musculus/" target="_blank">https://rest.ensembl.org/sequence/region/mus_musculus/</a><what_goes_here>:59522119..59523837:1?coord_system=seqlevel;content-type=text/x-fasta</div>
</div>
<div><br>
</div>
<div>-Allan.</div>
<div> </div>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>What would be the url to obtain the five_prime_UTR
region?</div>
<div><br>
</div>
<div>I have tried the URL below but it finds no slice.</div>
<div><a href="https://rest.ensembl.org/sequence/region/mus_musculus/GRCm39:59521583..59522118:1?coord_system=seqlevel;content-type=text/x-fasta" target="_blank">https://rest.ensembl.org/sequence/region/mus_musculus/GRCm39:59521583..59522118:1?coord_system=seqlevel;content-type=text/x-fasta</a> </div>
<div><br>
</div>
<div>-Allan.</div>
</div>
</div>
<br>
<fieldset></fieldset>
<pre>_______________________________________________
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</pre>
</blockquote>
<pre cols="72">--
Dr. Ben Moore (he/him)
Ensembl Outreach Manager
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK
<a href="mailto:bmoore@ebi.ac.uk" target="_blank">bmoore@ebi.ac.uk</a>
+44 (0)1223 494265</pre>
</div>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" rel="noreferrer" target="_blank">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a></blockquote><div><br></div><div><br></div><div>Thank you Ben, for the solution and advice.</div><div><br></div><div>- Allan.</div></div></div>