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</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Guillermo<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I am not part of the ensemble Dev team… but I have already implemented a plugin that retrieves Grantham scores. I based it on the Blosum62 plugin… but basically gave it a different scoring matrix taken from the same paper as Chris referenced.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I hope it is useful to you..<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best regards<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><br>Duarte<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Guillermo Marco Puche<br><b>Sent:</b> 29 April 2013 09:05<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] VEP Grantham amino acid distance<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hello Chris,<br><br>As I said I'm implementing this as an Ensembl Variant Effect Predictor plugin.<br>Input is an VCF file.<br><br>Best regards,<br>Guillermo.<br><br>On 04/29/13 10:03, <a href="mailto:cj5@sanger.ac.uk">cj5@sanger.ac.uk</a> wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre>Hi Guillermo,<o:p></o:p></pre><pre>Not sure of your requrements, but if you want a simple lookup of a mtrix based upon the original paper,<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Grantham, R. Amino Acid Difference Formula to Help Explain Protein Evolution, Science 1974 Sep 6;185(4154):862-4.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>please see attached.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>regards<o:p></o:p></pre><pre>Chris Joyce<o:p></o:p></pre><pre><o:p> </o:p></pre><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre>Hello,<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>I'm trying to calculate Grantham AA distance as a VEP plugin.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Currently I'm doing it parsing HGSVp and calculating distance between<o:p></o:p></pre><pre>the two AA being parsed.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Do you guys believe there's an easier and more efficient way to do this?<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Thank you.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Best regards,<o:p></o:p></pre><pre>Guillermo.<o:p></o:p></pre><pre>_______________________________________________<o:p></o:p></pre><pre>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><o:p></o:p></pre><pre>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><o:p></o:p></pre><pre>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></pre><pre><o:p> </o:p></pre><p class=MsoNormal><br><br><br><o:p></o:p></p><pre>_______________________________________________<o:p></o:p></pre><pre>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><o:p></o:p></pre><pre>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><o:p></o:p></pre><pre>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></pre></blockquote></blockquote><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>-- <o:p></o:p></p><div style='border-top:dotted #AEB1A6 1.0pt;border-left:none;border-bottom:dotted #AEB1A6 1.0pt;border-right:none;padding:6.0pt 0cm 6.0pt 0cm;margin-top:4.5pt;margin-bottom:4.5pt'><p class=MsoNormal style='line-height:12.0pt'><span style='font-size:8.5pt;font-family:"Lucida Sans","sans-serif";color:#555555'><a href="http://i.imgur.com/1MjpCpe.png" title="Sistemas Genomicos"><span style='text-decoration:none'><img border=0 width=174 height=50 id="_x0000_i1025" src="cid:image001.png@01CE44BF.B0DD0480"></span></a></span><strong><span style='font-size:7.5pt;font-family:"Lucida Sans","sans-serif";color:#333333;text-transform:uppercase'>g.marco</span></strong><span style='font-size:8.5pt;font-family:"Lucida Sans","sans-serif";color:#555555'>: Informatician at <span class=MsoHyperlink>Sistemas Genómicos S.L</span><br>phone: <a href="callto:0034635197460">0034635197460</a><br>web: <a href="http://www.sistemasgenomicos.com">www.sistemasgenomicos.com</a><o:p></o:p></span></p></div></div></div></body></html>