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</o:shapelayout></xml><![endif]--></head><body lang=NL link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US>Hi,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>I have a question, I’m using VEP2.0 to translate SNP positions to amino acids positions in transcripts and then predicting if it is damaging or not using polyphen. I know that you also include polyphen annotations in the latest version of VEP. This causes my question/problem when I try to annotate the amino acids substitutions using my polyphen set up, I sometimes get errors, it says that the returned amino acids are not in the transcript. When I look in the VEP output, then it does return a polyphen annotation. I use a convert table from the UCSC to translate the ensemble transcript ID’s to Swissprot id’s.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>An example of this error:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Input for VEP:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>6 152453291 152453291 G/A +<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Output by VEP<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>6_152453291_G/A 6:152453291 A ENSG00000131018 ENST00000367257 NON_SYNONYMOUS_CODING 3998 3998 1333 T/I aCa/aTa rs35591210 SIFT=tolerated(0.06);PolyPhen=benign(0.004);Condel=deleterious(0.885)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Input to polyphen:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>Q8NF91-4 T I<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Output by Polyphen<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US>ERROR: Neither AA1 (T) nor AA2 (I) in input matches Q8NF91-4 query sequence residue (R) at position (1333)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>There are more of these errors in my polyphen input. Is this because you used another than the standard database for your polyphen annotations (not the unireff100 database)? Or is it because my conversions from ensemble transcript id to swissprot id’s aren’t correct? Or do you just convert the T into a R and then rerun the prediction? Or is it something completely different?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Regards,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Marc Jan Bonder<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Bioinformatician at the University Medical Centre Groningen<o:p></o:p></span></p></div></body></html>