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  • Prokka Annotation - How to use blast nr DB

    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?
    Last edited by iltisanni; 05-16-2018, 04:53 AM.

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