Analysis of pattern overlaps and exact computation of P-values of pattern occurrences numbers: case of Hidden Markov Models
Finding new functional fragments in biological sequences is a challenging problem. Methods addressing this problem commonly search for clusters of pattern occurrences that are statistically significant. A measure of statistical significance is the P-value of a number of pattern occurrences, i.e. the probability to find at least S occurrences of words from a pattern in a random text of length N generated according to a given probability model. All words of the pattern are supposed to be of same length.
p-value pattern occurrences hidden markov model pssm (pwm)