What do the E-values and Estimated Precision Values mean?
E-values should be considered an internal scoring scheme. We have benchmarked the system on an extensive set of known remote homologies and calculated how often a given e-value is assigned to true and false homology. This is the basis for our ‘Estimated precision’ calculation. A typical result will present an e-value and next to it, an estimated precision value. The estimated precision is the percentage of times a match with the given e-value was found to be a true homology. Thus 80% estimated precision says that, on our benchmark set, 80% of hits with an an e-value equal to or lower than that reported were correct homologues, and 20% were false positives. The simple way to interpret the estimated precision is – ‘The likelihood that the match is correct’.
