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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Dear Developers<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I created a simple script to output the exons of specific transcripts with NM ids.<o:p></o:p></p><p class=MsoNormal>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></p><p class=MsoNormal>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></p><p class=MsoNormal><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'><o:p> </o:p></span></em></p><p class=MsoNormal><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:<o:p></o:p></span></em></p><p class=MsoNormal><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>_001040409.1<o:p></o:p></p><p class=MsoNormal>NM_001167607.1<o:p></o:p></p><p class=MsoNormal>NM_001199987.1<o:p></o:p></p><p class=MsoNormal style='line-height:12.0pt;background:white;vertical-align:baseline'>NM_001204090.1<o:p></o:p></p><p class=MsoNormal>NM_001242881.1<o:p></o:p></p><p class=MsoNormal>NM_014249.2<o:p></o:p></p><p class=MsoNormal>NM_015584.3<o:p></o:p></p><p class=MsoNormal>NM_024728.2<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Can you tell me how to retrieve these from the database?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Here is the portion of my script I use to retrieve the data:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>foreach my $query_transcript (@transcripts_of_interest) {<o:p></o:p></p><p class=MsoNormal> chomp $query_transcript;<o:p></o:p></p><p class=MsoNormal> my $transcript = "";<o:p></o:p></p><p class=MsoNormal> if ($query_transcript =~ /ENST/i){<o:p></o:p></p><p class=MsoNormal> $transcript = $transcript_adaptor->fetch_by_stable_id("$query_transcript");<o:p></o:p></p><p class=MsoNormal> }<o:p></o:p></p><p class=MsoNormal> else{<o:p></o:p></p><p class=MsoNormal> ($transcript) = @{ $transcript_adaptor->fetch_all_by_external_name("$query_transcript”);<o:p></o:p></p><p class=MsoNormal> }<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal> unless ($transcript){<o:p></o:p></p><p class=MsoNormal> $progress->message("Query: $query_transcript failed");<o:p></o:p></p><p class=MsoNormal> next;<o:p></o:p></p><p class=MsoNormal> }<o:p></o:p></p><p class=MsoNormal> foreach my $exon ( @{ $transcript->get_all_Exons() } ) {<o:p></o:p></p><p class=MsoNormal> my $estring = feature2string($exon);<o:p></o:p></p><p class=MsoNormal> print "$query_transcript:\t$estring\n";<o:p></o:p></p><p class=MsoNormal> }<o:p></o:p></p><p class=MsoNormal> $next_update = $progress->update() if (++$j > $next_update);<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>}<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Best regards<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span lang=PT style='font-size:10.0pt;font-family:"Arial","sans-serif"'>Duarte Molha<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>