Analysis of pattern overlaps and exact computation of P-values of pattern occurrences numbers: case of Hidden Markov Models

Table 1 PSSM-based patterns of length 12

Pattern	$Fraction (ℋ)$		$OV (ℋ)$	$P (ℋ)$	N _AC	P -value
PSSM(12,9.63)	0.00001	169	14	57	468	2.1887831E-27
PSSM(12,8.69)	0.00003	503	22	125	1123	9.9588634E-22
PSSM(12,7.41)	0.0001	1682	49	395	3189	2.1630650E-16
PSSM(12,5.89)	0.0003	5045	157	1789	9070	3.9649240E-12
PSSM(12,4.01)	0.001	16835	488	8967	29297	2.0930535E-07
PSSM(12,2.04)	0.003	50490	1417	35313	83016	0.001494591

The number x in “PSSM(12,x)” denotes the cut-off. The P-values are given w.r.t. the text length and probability models described in the text of the paper. The intermediate values of $Fraction (ℋ)$ (0.003, 0.0003, etc. instead of more common 0.005, 0.0005, etc.) were chosen to obtain more homogeneous log-scale.

ISSN: 1748-7188