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</o:shapelayout></xml><![endif]--></head><body 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'>Thanks Thibaut Hourlier<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 just get very confused with all these IDS with the same format meaning different things!<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'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>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><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 style='margin-left:36.0pt'><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Thibaut Hourlier<br><b>Sent:</b> 25 May 2012 11:20<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] Missing IDS in ENSEMBL database<o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><p class=MsoNormal style='margin-left:36.0pt'>Dear Duarte,<o:p></o:p></p><div><p class=MsoNormal style='margin-left:36.0pt'>I went through the four first of your IDs:<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p><div><div><p class=MsoNormal style='margin-left:36.0pt'>On 25 May 2012, at 10:14, Duarte Molha wrote:<o:p></o:p></p></div><p class=MsoNormal style='margin-left:36.0pt'><br><br><o:p></o:p></p><div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Dear Developers<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I created a simple script to output the exons of specific transcripts with NM ids.<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>It works fine for all but a small list of IDS. The large majority of the failed IDS have been suppressed from NCBI<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Because they were found to be a “ <i>nonsense-mediated mRNA decay (NMD) candidate</i>” so I do not mind eliminating those records from my query.<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><em><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black;border:none windowtext 1.0pt;padding:0cm;background:white;font-style:normal'> </span></em><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><em><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black;border:none windowtext 1.0pt;padding:0cm;background:white;font-style:normal'>However some of the ones that fail are in NCBI database and for some reason ENSEMBL is not able to query them:</span></em><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><em><span style='font-size:10.0pt;font-family:"Arial","sans-serif";color:black;border:none windowtext 1.0pt;padding:0cm;background:white;font-style:normal'>NM</span></em><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>_001040409.1<o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-left:36.0pt'>It is an NMD transcript.<br><br><o:p></o:p></p><div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>NM_001167607.1<o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-left:36.0pt'>It is an exon supporting feature and not a transcript supporting feature, i think this is the reason you don't get it with your script<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><a href="http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000196743;r=5:150591711-150650001;t=ENST00000523466">http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000196743;r=5:150591711-150650001;t=ENST00000523466</a><br><br><o:p></o:p></p><div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>NM_001199987.1<o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-left:36.0pt'>If you look in the Gene database at NCBI you will see that there is 2 other sequences for NDUFB6, which are the transcript supporting feature for the 2 transcripts in Ensembl for the gene.<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><a href="http://www.ncbi.nlm.nih.gov/gene/?term=NM_001199987.1">http://www.ncbi.nlm.nih.gov/gene/?term=NM_001199987.1</a><o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><a href="http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000165264;r=9:32552997-32573160;t=ENST00000379847">http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000165264;r=9:32552997-32573160;t=ENST00000379847</a><br><br><o:p></o:p></p><div><div><p class=MsoNormal style='margin-left:36.0pt;line-height:12.0pt;background:white;vertical-align:baseline'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>NM_001204090.1<o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-left:36.0pt'>Same problem as above, we did not use this sequence.<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>What you can do is to use the HGNC identifier of these failing IDs in the fetch_all_by_external_id method, i.e. NM_001199987.1 -> NDUFB6<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>Regards<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'>Thibaut<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><br><br><o:p></o:p></p><div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>NM_001242881.1<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>NM_014249.2<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>NM_015584.3<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>NM_024728.2<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Can you tell me how to retrieve these from the database?<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Here is the portion of my script I use to retrieve the data:<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>foreach my $query_transcript (@transcripts_of_interest) {<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> chomp $query_transcript;<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> my $transcript = "";<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> if ($query_transcript =~ /ENST/i){<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> $transcript = $transcript_adaptor->fetch_by_stable_id("$query_transcript");<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> }<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> else{<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> ($transcript) = @{ $transcript_adaptor->fetch_all_by_external_name("$query_transcript”);<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> }<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> unless ($transcript){<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> $progress->message("Query: $query_transcript failed");<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> next;<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> }<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> foreach my $exon ( @{ $transcript->get_all_Exons() } ) {<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> my $estring = feature2string($exon);<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> print "$query_transcript:\t$estring\n";<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> }<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> $next_update = $progress->update() if (++$j > $next_update);<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>}<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Best regards<o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span lang=PT style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Duarte Molha</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'><o:p></o:p></span></p></div><div><p class=MsoNormal style='margin-left:36.0pt'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p></div><p class=MsoNormal style='margin-left:36.0pt'>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>List admin (including subscribe/unsubscribe):<span class=apple-converted-space> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog:<span class=apple-converted-space> </span><a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></p></div></div><p class=MsoNormal style='margin-left:36.0pt'><o:p> </o:p></p></div></div></body></html>