I am trying to annotate a number of genomes and want to add specific annotations from my own FASTA db which includes specific virulence genes.
One protein in my own fasta database is cstB (an outer membrane usher that share conserved motifs with other ushers). In one genome there should only be one cstB but when I'm running prokka I get 7 cstB. There are 6 CDSs that are annotated as cstB that shouldn't be. Is there a way to specify --coverage or --evalue specifically for the proteins in the .faa file to make the annotation more specific but at the same time not change the matching for proteins in the databases used by prokka?
For example using --coverage 95 fixes the issue with the 7 cstB but I assume also affects the annotation of the other proteins not inlcuded in my own FASTA database, yes?
Hi,
I am trying to annotate a number of genomes and want to add specific annotations from my own FASTA db which includes specific virulence genes.
One protein in my own fasta database is cstB (an outer membrane usher that share conserved motifs with other ushers). In one genome there should only be one cstB but when I'm running prokka I get 7 cstB. There are 6 CDSs that are annotated as cstB that shouldn't be. Is there a way to specify --coverage or --evalue specifically for the proteins in the .faa file to make the annotation more specific but at the same time not change the matching for proteins in the databases used by prokka? For example using --coverage 95 fixes the issue with the 7 cstB but I assume also affects the annotation of the other proteins not inlcuded in my own FASTA database, yes?
Best regards, Astrid