David Coil edited Organism Identification using 16s rRNA gene sequence.md  over 9 years ago

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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. Figure \ref{fig:GOLD\_results} shows an example screen shot of the results for "_Brachybacterium_." Clicking on a project ID will take you to a more detailed description of the project including its project status (complete, permanent draft, incomplete, targeted). While some "incomplete" and "targeted" projects will be completed, many will not, so we tend to ignore these categories.  If you have relatively ambiguous identification results (_e.g_. you think you have some sort of _Brachybacterium_ but aren't sure which species,) it could be worthwhile to perform an alignment of your 16S sequence with those from genomes already in Genbank. Genbank or to built a phylogenetic tree as in Section 11.  ##Align 16S Sequences using Align Sequences Nucleotide BLAST  First locate the 16S sequences of the genome you'd like to compare to, by searching the NCBI Nucleotide database for "Species 16s gene".