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<body class='hmmessage'><div dir='ltr'><span style="font-size: 12.7272720336914px; color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; line-height: 16px;">Hi, </span><br style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: small;"><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: small;"><span style="color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; font-size: 12.7272720336914px; line-height: 16px;">I am trying to fetch the prediction matrix for some proteins, and then some polyphen predictions for some particular aminoacid changes. In Ensembl Help Documentation of predicted data, it is found: "</span><span style="font-size: 12.7272720336914px; color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; line-height: 16px;">Prediction matrices can be fetched and manipulated in a user-friendly manner using the variation API, specifically using the </span><i style="font-size: 12.7272720336914px; color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; line-height: 16px;">ProteinFunctionPredictionMatrixAdaptor</i><span style="font-size: 12.7272720336914px; color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; line-height: 16px;"> which allows you to fetch a prediction matrix using either a transcript or a translation stable ID. This adaptor returns a </span><i style="font-size: 12.7272720336914px; color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; line-height: 16px;">ProteinFunctionPredictionMatrix</i><span style="font-size: 12.7272720336914px; color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; line-height: 16px;"> object and you can use the </span><i style="font-size: 12.7272720336914px; color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; line-height: 16px;">get_prediction</i><span style="font-size: 12.7272720336914px; color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; line-height: 16px;"> method to retrieve a prediction for a given position and amino acid". </span></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: small;"><span style="font-size: 12.7272720336914px; color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; line-height: 16px;"><br></span></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: small;"><span style="font-size: 12.7272720336914px; color: rgb(85, 85, 85); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; line-height: 16px;">However, I am not able to get my matrix using any type of ID. I have been trying fetch_polyphen_predictions_by_translation_md5 (using Perl </span><font color="#555555" face="Luxi Sans, Helvetica, Arial, Geneva, sans-serif"><span style="line-height: 16px;">Digest::MD5 to get md5_hex), and it returns a matrix, but the predictions doesn't match the real ones that polyphen predicts for this change (I checked on their website). </span></font></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: small;"><font color="#555555" face="Luxi Sans, Helvetica, Arial, Geneva, sans-serif"><span style="line-height: 16px;">I would appreciate helps/tips to make things easier or to point out where is my mistake. Here is so far what I wrote: </span></font></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: small;"><font color="#555555" face="Luxi Sans, Helvetica, Arial, Geneva, sans-serif"><span style="line-height: 16px;"><div><br></div><div>use warnings;</div><div>use Bio::EnsEMBL::Registry;</div><div>use Digest::MD5 qw(md5 md5_hex md5_base64);</div><div>use Bio::EnsEMBL::Utils::Exception qw(throw warning);</div><div>use Bio::EnsEMBL::Variation::ProteinFunctionPredictionMatrix;</div><div>print "Loading Registry...\n";</div><div>my $registry = "Bio::EnsEMBL::Registry";</div><div>$registry->load_registry_from_db( -host => 'ensembldb.ensembl.org', -user => 'anonymous');</div><div>print "Correctly Loaded Registry\n";</div><div>my $transcript_adaptor = $registry -> get_adaptor ('Human', 'Core', 'Transcript');</div><div>my $matrix_adaptor= $registry-> get_adaptor ('Human', 'variation', 'ProteinFunctionPredictionMatrixAdaptor');</div><div>my $transcript= $transcript_adaptor -> fetch_by_stable_id('ENST00000367429');</div><div>my $translation_md5 = md5_hex($transcript->translate->seq());</div><div>my $matrix_prediction= $matrix_adaptor-> fetch_polyphen_predictions_by_translation_md5($translation_md5);</div><div>my ($prediction) = $matrix_prediction ->get_prediction(1, V);</div><div>print "$prediction\n";</div><div><br></div><div>You will see that the outcome is benign, and it should be probably damaging.</div><div><br></div><div>Thanks for the help, </div><div><br></div><div>Oriol</div></span></font></div> </div></body>
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