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A P-value associated to a result is the estimate of how likely the result could be observed by chance alone. P-values are preferable to unnormalized scores because users can determine the amout of risk they are willing to take in looking (and following up) with the matches.

There are many publications about P-value calculations for alignment-based similarity search methods. This is a very partial list:


  1. Mott, R. Accurate Formula for P-values of gapped local sequence and prole alignments [[1]]
  2. Stephen F. Altschul, Ralf Bundschuh, Rolf Olsen and Terence Hwa. The estimation of statistical parameters for local alignment score distributions [[2]]
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