Interpretation of threshold setting in HMMER

ABC 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
   reference.

   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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