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  • RDP II - taxonomy

    Hi,

    I have RDP II release11_2_Bacteria_unaligned.gb. The file has taxonomy written, for example, like:

    SOURCE Agromyces ramosus
    ORGANISM Agromyces ramosus
    Root; Bacteria; "Actinobacteria"; Actinobacteria; Actinobacteridae;
    Actinomycetales; Micrococcineae; Microbacteriaceae; Agromyces.


    For this I manually obtained taxonomy nomenclature (root, domain, phylum, class, subclass, order, suborder, family, genus):

    root
    domain Bacteria
    phylum "Actinobacteria"
    class Actinobacteria
    subclass Actinobacteridae
    order Actinomycetales
    suborder Micrococcineae
    family Microbacteriaceae
    genus Agromyces

    However, I can also see entries like (root, domain, phylum, class, order, family, genus):

    root
    domain Bacteria
    phylum Firmicutes
    class Bacilli
    order Lactobacillales
    family Streptococcaceae
    genus Streptococcus

    How can I assign nomenclature for each bacteria in the RDP II gb file?

    Thanks

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