Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • sampie
    Member
    • Jun 2014
    • 10

    #1

    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

Latest Articles

Collapse

  • kinpict.com
    Reply to 16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by kinpict.com
    The part about this topic feels surprisingly grounded, and the details on the page is the bit that made me slow down. I’d keep <a href="https://kinpict.com/">ai family photo generator</a> bookmarked for later.
    Today, 06:37 PM
  • SEQadmin2
    16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
    by SEQadmin2





    NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...
    10-30-2026, 06:46 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 11-12-2026, 07:59 AM
0 responses
27 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 11-05-2026, 09:25 AM
0 responses
35 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 11-03-2026, 11:54 AM
2 responses
56 views
0 reactions
Last Post kinpict.com  
Started by SEQadmin2, 10-28-2026, 09:57 AM
0 responses
175 views
0 reactions
Last Post SEQadmin2  
Working...