Hi out there. We posted this awhile back and got no response. Does anyone have any suggestions at all on our problem with UTR regions not displaying correctly with exons made up partly of a CDS region and a UTR region in GFF3?
--Bob Muller, TAIR Amie Radenbaugh wrote: > Hi All, > > We are having trouble getting the FastaDumper plug-in to work in parallel > with our other CDS and mRNA (Protein Coding) tracks. When we first added the > FastaDumper plug-in to the .conf file, all of the basic functionality worked, > but when trying to download a decorated FASTA file for a CDS sequence, the > FastaDumper failed to label the CDS regions correctly. We then introduced a > new element to our .gff file which specifies an entire CDS span (translation > start to translation end) as other groups such as FlyBase have done. This > fixed the problem with labeling the CDS regions using the FastaDumper, but it > introduced new problems on our mRNA track. The UTR regions do not get > displayed correctly when an exon is made up partly of a CDS region and partly > of a UTR region. > > Here is an excerpt from our GFF3 file where the problem occurs: > > Chr1 TAIR71 chromosome 1 30432563 . . . > ID=Chr1;Name=Chr1 > Chr1 TAIR71 gene 1512900 1518804 . - . > ID=AT1G05230;Note=protein_coding_gene;Name=AT1G05230 > Chr1 TAIR71 mRNA 1512900 1517247 . - . > ID=AT1G05230.1;Parent=AT1G05230;Name=AT1G05230.1;Index=1 > Chr1 TAIR71 protein 1513387 1517023 . - . > ID=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1;Derives_from=AT1G05230.1 > Chr1 TAIR71 exon 1517175 1517247 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 five_prime_UTR 1517175 1517247 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 exon 1516782 1517056 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 five_prime_UTR 1517024 1517056 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 CDS 1516782 1517023 . - 0 > Parent=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1-CDS > Chr1 TAIR71 exon 1516586 1516703 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 CDS 1516586 1516703 . - 1 > Parent=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1-CDS > Chr1 TAIR71 exon 1515820 1516008 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 CDS 1515820 1516008 . - 0 > Parent=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1-CDS > Chr1 TAIR71 exon 1515037 1515450 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 CDS 1515037 1515450 . - 0 > Parent=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1-CDS > Chr1 TAIR71 exon 1514861 1514962 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 CDS 1514861 1514962 . - 0 > Parent=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1-CDS > Chr1 TAIR71 exon 1514589 1514789 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 CDS 1514589 1514789 . - 0 > Parent=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1-CDS > Chr1 TAIR71 exon 1514349 1514523 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 CDS 1514349 1514523 . - 0 > Parent=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1-CDS > Chr1 TAIR71 exon 1513993 1514264 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 CDS 1513993 1514264 . - 2 > Parent=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1-CDS > Chr1 TAIR71 exon 1513824 1513919 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 CDS 1513824 1513919 . - 0 > Parent=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1-CDS > Chr1 TAIR71 exon 1513373 1513743 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 CDS 1513387 1513743 . - 0 > Parent=AT1G05230.1-CDS_SPAN;Name=AT1G05230.1-CDS > Chr1 TAIR71 three_prime_UTR 1513373 1513386 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 exon 1512900 1513292 . - . > Parent=AT1G05230.1 > Chr1 TAIR71 three_prime_UTR 1512900 1513292 . - . > Parent=AT1G05230.1 > > Here are our CDS and mRNA tracks: > > [ProteinCoding] > feature = mRNA > glyph = processed_transcript > bgcolor = steelblue > fgcolor = blue > utr_color = lightblue > label density = 50 > bump density = 150 > description = 0 > link = /servlets/TairObject?name=$name&type=gene > key = Protein Coding Gene Models > category = Gene > citation = This track shows the transcript of the genes in this > section of the chromosome. > > [CDS] > feature = protein > glyph = cds > height = 30 > sixframe = 1 > ignore_empty_phase = 1 > frame0f = cadetblue > frame1f = blue > frame2f = darkblue > frame0r = darkred > frame1r = red > frame2r = crimson > category = Gene > key = CDS > citation = This track shows coding segments for the genes in this > section of the chromosome. > > We are using Bio::DB::SeqFeature::Store. It would be great if anyone has any > tips on how to get the FastaDumper working together with the appropriate > labeling of CDS and mRNA tracks. > > Thanks, > Amie > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Gmod-gbrowse mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Gmod-gbrowse mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
