Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Hi all
According to their instructions, it accepts a variety of file format types including GFF3.
Hence I used GFF3 files for DNAplotter.
The example of GFF3 is shown below.
I tried to visualize this gff3 file, however, got the error messages:
while reading from Blast2GO_gff_1.gff: gene can't have seqName as a qualifier
while reading from Blast2GO_gff_1.gff: gene can't have HintSupport as a qualifier
while reading from Blast2GO_gff_1.gff: mRNA can't have score as a qualifier
while reading from Blast2GO_gff_1.gff: transcription_start_site is not a valid key
while reading from Blast2GO_gff_1.gff: start_codon is not a valid key
while reading from Blast2GO_gff_1.gff: stop_codon is not a valid key
while reading from Blast2GO_gff_1.gff: transcription_end_site is not a valid key
Hi all According to their instructions, it accepts a variety of file format types including GFF3. Hence I used GFF3 files for DNAplotter. The example of GFF3 is shown below.
gff-version 3
gff generated with Blast2GO
Number of FASTA deflines: 3990
6 AUGUSTUS gene 706 4825 0.14 + . ID=6.g1; seqName=6.g1; HintSupport=0 6 AUGUSTUS mRNA 706 4825 0.14 + . ID=6.g1.t1; Parent=6.g1; seqName=6.g1; HintSupport=0 6 AUGUSTUS transcription_start_site 706 706 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS exon 706 825 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS exon 3777 4048 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS start_codon 3783 3785 . + 0 Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS intron 4049 4163 0.36 + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS intron 4219 4305 0.97 + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS CDS 3783 4048 0.47 + 0 ID=6.g1.t1.cds; Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS CDS 4164 4218 0.36 + 1 ID=6.g1.t1.cds; Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS exon 4164 4218 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS CDS 4306 4575 0.94 + 0 ID=6.g1.t1.cds; Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS exon 4306 4825 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS stop_codon 4573 4575 . + 0 Parent=6.g1.t1; seqName=6.g1; HintSupport=0 6 AUGUSTUS transcription_end_site 4825 4825 . + . Parent=6.g1.t1; seqName=6.g1; HintSupport=0
I tried to visualize this gff3 file, however, got the error messages:
while reading from Blast2GO_gff_1.gff: gene can't have seqName as a qualifier while reading from Blast2GO_gff_1.gff: gene can't have HintSupport as a qualifier while reading from Blast2GO_gff_1.gff: mRNA can't have score as a qualifier while reading from Blast2GO_gff_1.gff: transcription_start_site is not a valid key while reading from Blast2GO_gff_1.gff: start_codon is not a valid key while reading from Blast2GO_gff_1.gff: stop_codon is not a valid key while reading from Blast2GO_gff_1.gff: transcription_end_site is not a valid key
best,