Jenna M. Lang edited Organism Identification using 16s rRNA gene sequence.md  about 10 years ago

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##Interpreting the results  Depending on the quality of the Sanger sequencing and the particular bacteria sequenced, the BLAST results can range from definitive to relatively uninformative. Examples of both are discussed below.  1. In Figure X, FigureX,  it is not necessary to build a phylogenetic tree for further identification. All of the top hits are either Kocuria rosea or Kocuria sp have e-values of 0.0, perfect query coverage, and 99% to100% identity. In this case, proceed to "Using GOLD". 2. In Figure Y FigureX  the results are much more ambiguous. The results show more than 99% identity to multiple species within multiple genera. In this case, proceed to "Making a Phylogenetic Tree", before using GOLD. ##Using GOLD  Navigate to:  http://genomesonline.org/cgi-bin/GOLD/index.cgi  Click the search button on the left side of the page and you should be taken to a page that looks like the screen shot displayed in FigureX.  Fill out the blue Organism Information (Organism Name) section, with information about your microbe from BLAST and click submit search. We usually search for only the genus to get a sense for how well that genus is represented in the database and which species are present. FigureX shows an example screen shot of the results for "Lysinibacillus"