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<p class="MsoNormal">Hi, <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have a question about inconsistencies between the Ensembl website and the Ensembl REST API. I am querying from
<a href="https://rest.ensembl.org/">https://rest.ensembl.org/</a> using <a href="https://rest.ensembl.org/documentation/info/sequence_id">
<span style="font-size:10.5pt;font-family:"Helvetica Neue";color:#0088CC;text-decoration:none">GET sequence/id/:id</span></a> without defining any optional arguments, but I often get results that differ from the website.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here are two examples:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">For Ensembl ID ENSTGUG00000006139, the REST API returns:<o:p></o:p></p>
<p class="MsoNormal">Description: <span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">
primary_assembly:bTaeGut1_v1.p:1:107513</span><b><span style="font-size:10.5pt;font-family:"Courier New";color:red;background:white">7</span></b><span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">86:107528</span><b><span style="font-size:10.5pt;font-family:"Courier New";color:red;background:white">1</span></b><span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">06:-1<o:p></o:p></span></p>
<p class="MsoNormal">Sequence:<span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white"> CTCAGCACCGGCCAACATGGCGGCG…</span><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">However, the <a href="https://uswest.ensembl.org/Taeniopygia_guttata/Gene/Sequence?db=core;g=ENSTGUG00000006139;r=1:107513786-107528106">
Ensembl website</a> finds:<o:p></o:p></p>
<pre style="margin-bottom:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Description: </span><span style="font-size:10.5pt;color:#212121;background:white">primary_assembly:bTaeGut1_v1.p:1:107513</span><b><span style="font-size:10.5pt;color:red;background:white">1</span></b><span style="font-size:10.5pt;color:#212121;background:white">86:107528</span><b><span style="font-size:10.5pt;color:red;background:white">7</span></b><span style="font-size:10.5pt;color:#212121;background:white">06:-1<br></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Sequence:</span><span style="color:black"> </span><span style="font-size:10.5pt;color:#212121;background:white">TTGAGCATCACAATACAAGAAACACATT…<o:p></o:p></span></pre>
<pre style="margin-bottom:12.0pt;background:white"><span style="font-size:10.5pt;color:#212121;background:white"><o:p> </o:p></span></pre>
<p class="MsoNormal">For Ensembl ID ENSG00000239862, the REST API returns:<o:p></o:p></p>
<p class="MsoNormal">Description: <span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">
chromosome:GRCh38:2:8929</span><b><span style="font-size:10.5pt;font-family:"Courier New";color:red;background:white">72</span></b><span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">64:8929</span><b><span style="font-size:10.5pt;font-family:"Courier New";color:red;background:white">77</span></b><span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">85:-1</span><o:p></o:p></p>
<p class="MsoNormal">Sequence: <span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">
AGGCTGGTCACACCCCGTGCAGCAGTCAGT…</span><o:p></o:p></p>
<p class="MsoNormal" style="line-height:14.25pt;background:#FFFFFE"><o:p> </o:p></p>
<p class="MsoNormal">However, the <a href="https://uswest.ensembl.org/Homo_sapiens/Gene/Sequence?db=core;g=ENSG00000239862;r=2:89297264-89297785;t=ENST00000465170">
Ensembl website</a> finds:<o:p></o:p></p>
<p class="MsoNormal" style="line-height:14.25pt;background:#FFFFFE"><span style="color:black">Description:
</span><span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">chromosome:GRCh38:2:8929</span><b><span style="font-size:10.5pt;font-family:"Courier New";color:red;background:white">66</span></b><span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">64:8929</span><b><span style="font-size:10.5pt;font-family:"Courier New";color:red;background:white">83</span></b><span style="font-size:10.5pt;font-family:"Courier New";color:#212121;background:white">85:-1<o:p></o:p></span></p>
<pre style="margin-bottom:12.0pt;background:white"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Sequence:</span><span style="font-family:"Calibri",sans-serif;color:black"> </span><span style="font-size:10.5pt;color:#212121;background:white">AAAAATATTCCCCTGGCTGGACGTGGTGGCTCAT…<o:p></o:p></span></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Both the description and the sequence are inconsistent. <o:p>
</o:p></p>
<p class="MsoNormal">Do the website and the REST API source from different data bases?
<o:p></o:p></p>
<p class="MsoNormal">Which one is correct?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">With best regards,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Laura<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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