deletions | additions       diff --git a/Organism Identification using 16s rRNA gene sequence.md b/Organism Identification using 16s rRNA gene sequence.md  index 7034ca5..4a5602b 100644  --- a/Organism Identification using 16s rRNA gene sequence.md  +++ b/Organism Identification using 16s rRNA gene sequence.md 
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1. In some cases it is not necessary to build a phylogenetic tree for further identification. If all of the top hits are the same species (or end in sp.), have e-values of 0.0, good query coverage, and 99% to 100% identity you can proceed to "Using GOLD".  2. In other cases the results are much more ambiguous. The results may show more than 99% identity to multiple species within multiple genera. In this case, proceed to section 11 "Building a 16S rDNA Phylogenetic Tree", before using GOLD.  3. Another possibility is that you get significantly less than 99% identity to any sequences at NCBI. One explanation is poor quality sequence, this might require more stringent trimming or even resequencing if the quality is bad enough to make assigning taxonomy difficult. Another possibility is having isolated something that is not that closely related to anything in the database. In the latter case we would recommend first re-doing the BLAST but unchecking the "Uncultured/environmental sample" to see if the sequence matches others that have been found, but are not associated with a cultured organism. In either case, we would recommend re-sequencing for confirmation and then proceeding to section 11 "Building a 16S rDNA Phylogenetic Tree" to examine the phylogenetic context of the new novel  sequence. ##Using GOLD (the Genomes Online Database)  Go to: http://genomesonline.org/cgi-bin/GOLD/index.cgi