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Old 08-23-2014, 11:26 PM   #1
sampie
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Location: Finland

Join Date: Jun 2014
Posts: 10
Default 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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