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Jenna M. Lang added Organism Identification using 16s rRNA gene sequence.md
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#Organism Identification using 16s rRNA gene sequence
In a classroom or undergraduate research setting the project may not have a particular bacterial species in mind. In this case it is necessary to screen the 16S Sanger sequencing results for possible genome sequencing candidates. We recommend starting with BLAST results, then continuing onto the Genomes Online Database (GOLD), and simply Google searching. In many cases it will be handy to also build a phylogenetic tree to aid in identification since the 16S results may not be sufficiently informative.
##BLAST 16S rDNA sequence
Begin by navigating to the Standard Nucleotide BLAST at NCBI:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE\_TYPE=BlastSearch&LINK_LOC=blasthome
Paste in your consensus sequence. We recommend checking the box to exclude Uncultured/environmental sample sequences since these will not be informative for identification. Be sure the nucleotide collection (nr/nt) is selected under database and click the BLAST button.
