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Table 3 Comparison of p-values calculated by the AHOPRO program, by Monte Carlo simulation and by compound Poisson distribution formula under the M1 model

From: Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

MOTIF, CUTOFF

OCC.

AHOPRO

MONTE CARLO

POISSON

AHOPRO/MC

AHOPRO/POISSON

bcd, 5.3

3

0.013

0.014

0.012

0.998

1.11

kr, 5.0

4

0.011

0.011

0.008

1.01

1.43

hb, 6.2

2

0.14

0.14

0.11

0.9987

1.25

bcd & kr

3&4

0.00051

0.00051

9.62E-05

0.9991

5.34

bcd & kr & hb

3&4&2

6.9E-05

6.97E-05

1.08E-05

0.9889

6.36

  1. Comparison of p-values calculated by the AHOPRO program for the Markov(1) model with those calculated by Monte Carlo simulations and by Poisson formula for motifs of D. melanogaster developmental transcription factors bicoid, kruppel, and hunchback.
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Algorithms for Molecular Biology

ISSN: 1748-7188