Table of Contents
Gene Regulation
The Gibbs Sampler
Entering the Data
Advanced Option
s
More Advanced Options
Prokaryotic and Eukaryotic Defaults
Processing Sequences
Calculating Counts
Site Sampler
Equation 1: Motif Probability
Equation 2: Background Probability
Equation 3: Odds
Equation 4: Motif Element Probability
Motif Sampler
Recursive Sampler
Centroid Sampler
The MAP
Fragmentation
Near Optimal Sampling
MAP Maximization
Sample Results
Example 1: Porin Data
Example 2: Dinucleotide Data
Example 3: CRP Data
Example 4: Full Crp Results
Example 5: Output from the Centroid Sampler
Example 6: Prokayotic Phylogenetic Footprinting
Example 7: Prokaryotic Co-expression Data
Appendix A
Possible Errors
Names and Abbreviations of the Common Amino Acids
References
Gibbs home page
Gibbs home page