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Hi,
I want to annotate an assembled Pseudomonas Genome (fasta) with prokka.
I was successfull so far but I'm not sure where the information comes from.
I first downloaded a related protein-fasta from NCBI and told prokka to use that file with the --protein option.
Now what is prokka doing when it finds an unknown cds? Where does it search?
Is it possible to tell prokka to search in a local downloaded nr blast database?
maybe it is possible to replace or expand the prokka-used databases by the nr blast db? (I recognized the internal prokka dbs and the nr blast db have different file extensions)
My idea is:
Search for all cds in my downloaded, related protein-fasta and at the end to search for all unknown cds in the nr blast database.
Is that possible?
I want to annotate an assembled Pseudomonas Genome (fasta) with prokka.
I was successfull so far but I'm not sure where the information comes from.
I first downloaded a related protein-fasta from NCBI and told prokka to use that file with the --protein option.
Now what is prokka doing when it finds an unknown cds? Where does it search?
Is it possible to tell prokka to search in a local downloaded nr blast database?
maybe it is possible to replace or expand the prokka-used databases by the nr blast db? (I recognized the internal prokka dbs and the nr blast db have different file extensions)
My idea is:
Search for all cds in my downloaded, related protein-fasta and at the end to search for all unknown cds in the nr blast database.
Is that possible?