Hi,
I am seeking opinions on the best way to determine OTU identity using Blastn. Would the best way to identify an OTU be to blast the OTU to the full nr/nt Nucleotide collection or to blast your OTU to a reduced database made up of sequences that target your organism of interest (for example, the organism to which you designed the sequencing primers for)?
An example to clarify the question:
Scenario 1: You blast your OTU to the full nr/nt Nucloetide collection and get the following best hit: Homo sapiens with an E-value of 3e-175.
Scenario 2: You then blast the same OTU to a database made up of only reads for your organism of interest (Pan troglodytes). The hit you get is for Pan troglodytes with an E-value of 1e-40.
Both E-values suggest that the hit is significant and not due to random chance (http://sfg.stanford.edu/BLAST.html), but the Homo sapiens result is a better match due to its smaller E-value. However, if you know that you should only have matches to Pan troglodytes, is it justifiable to use the less significant match? Which approach is better?
Thanks in advance for any opinions.
You have sequenced some marker gene but assign taxonomy by blastn against a non-marker gene specific database? This is wrong on so many levels..