I used Prokka via Galaxy Europe to annotate de novo bacterial genome assemblies. I loaded the genbank-files into Clone Manager in order to rotate the molecule so that the dnaA gene (according to the initial Prokka annotation) is the first open reading frame. Then I exported the molecule as fasta and re-annotated the genome using Prokka via Galaxy Europe. Surprisingly, this resulted in a decreased number of CDS (the genome size did not change) for both assemblies.
1st assembly before rotation to dnaA
organism: Genus species strain
contigs: 1
bases: 9719866
CDS: 7060
gene: 7144
rRNA: 3
repeat_region: 2
tRNA: 80
tmRNA: 1
1st assembly after rotation to dnaA
organism: Genus species strain
contigs: 1
bases: 9719866
CDS: 7040
gene: 7124
rRNA: 3
repeat_region: 2
tRNA: 80
tmRNA: 1
2nd assembly before rotation to dnaA
organism: Genus species strain
contigs: 1
bases: 7031387
CDS: 5560
gene: 5639
rRNA: 8
repeat_region: 1
tRNA: 71
**2nd assembly after rotation to dnaA*
organism: Genus species strain
contigs: 1
bases: 7031387
CDS: 5557
gene: 5636**
rRNA: 8
repeat_region: 1
tRNA: 71
I have also noticed that in one case, the dnaA gene was now 18 bp shorter. As the DNA sequence is the same (only rotated) I expected that the annotation would be identical and reproducible.
Why is this happening and how can I avoid it in the future?
Thank you in advance for your help.
Hallo,
I used Prokka via Galaxy Europe to annotate de novo bacterial genome assemblies. I loaded the genbank-files into Clone Manager in order to rotate the molecule so that the dnaA gene (according to the initial Prokka annotation) is the first open reading frame. Then I exported the molecule as fasta and re-annotated the genome using Prokka via Galaxy Europe. Surprisingly, this resulted in a decreased number of CDS (the genome size did not change) for both assemblies.
1st assembly before rotation to dnaA organism: Genus species strain contigs: 1 bases: 9719866 CDS: 7060 gene: 7144 rRNA: 3 repeat_region: 2 tRNA: 80 tmRNA: 1
1st assembly after rotation to dnaA organism: Genus species strain contigs: 1 bases: 9719866 CDS: 7040 gene: 7124 rRNA: 3 repeat_region: 2 tRNA: 80 tmRNA: 1
2nd assembly before rotation to dnaA organism: Genus species strain contigs: 1 bases: 7031387 CDS: 5560 gene: 5639 rRNA: 8 repeat_region: 1 tRNA: 71
**2nd assembly after rotation to dnaA* organism: Genus species strain contigs: 1 bases: 7031387 CDS: 5557 gene: 5636** rRNA: 8 repeat_region: 1 tRNA: 71
I have also noticed that in one case, the dnaA gene was now 18 bp shorter. As the DNA sequence is the same (only rotated) I expected that the annotation would be identical and reproducible.
Why is this happening and how can I avoid it in the future? Thank you in advance for your help.
Best regards,
Jonathan