Interpretation of threshold setting in HMMER
cdcer at hongkong.com
Tue Nov 11 13:24:28 EST 2003
By using HMMER, a threshold is set to limit the output result.
The default value for the threshold is 10. I would like to ask
what is the meaning of this value, 10? It should be a parameter
to measure how close (large probability) the between the
reference (model) and the query. Therefore, my question is do
we have some equivalent examples to understand such idea. What
I am trying to say is
ref: 1 2 3 4 5
query: 1 1 3 4 5
In above example, both of them have 5 bits, and 4 are the same,
so, we could conclude that query is 80\% similar to the
By the same token, what does 10 mean in this sense, could I
construct an example to show the idea?
Thank you very much!
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