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David Coil edited Organism Identification using 16s rRNA gene sequence.md
almost 10 years ago
Commit id: df9997b547d456ec31c5fc0cabbbcf849bb8b203
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http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE\_TYPE=BlastSearch&LINK_LOC=blasthome
Paste in your
Sanger 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.
##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 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 sp, have e-values of 0.0, perfect query coverage, and 99%
to100% to 100% identity. In this case, proceed to "Using GOLD".
2. In 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