Example Models and Sequences

##Dice Model (Dishonest Casino Model) Dice model from pg 65 of R Durbin, S.Eddy, A. Krogh, and G. Mitchison.,"Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids." Cambridge Press, UK (1998)

#STOCHHMM MODEL FILE
MODEL INFORMATION
======================================================
MODEL_NAME:	CASINO DICE MODEL
MODEL_DESCRIPTION:	Taken from CH3 Durbin/Eddy
MODEL_CREATION_DATE:	August 28,2009

TRACK SYMBOL DEFINITIONS
======================================================
DICE:	1,2,3,4,5,6

STATE DEFINITIONS
#############################################
STATE:	
	NAME:	INIT
TRANSITION:	STANDARD: P(X)
	FAIR:	0.5
	LOADED:	0.5
#############################################
STATE:	
	NAME:	FAIR
	PATH_LABEL:	F
	GFF_DESC:	FAIR
TRANSITION:	STANDARD: P(X)
	FAIR:	0.95
	LOADED:	0.05
	END:	1
EMISSION:	DICE: P(X)
	ORDER:	0
@1	2	3	4	5	6
0.167	0.167	0.167	0.167	0.167	0.167
#############################################
STATE:
	NAME:	LOADED
	PATH_LABEL:	L
	GFF_DESC:	LOADED
TRANSITION:	STANDARD: P(X)
	FAIR:	0.1
	LOADED:	0.9
	END:	1
EMISSION:	DICE: P(X)
	ORDER:	0
@1	2	3	4	5	6	
0.1	0.1	0.1	0.1	0.1	0.5
#############################################
//END

##GC-rich Sequence Model Created from Problem 3.16 of M. Borodovsky and S. Ekisheva., "Problems and Solutions in Biological Sequence Analysis.", Cambridge Press, UK (2006)

#STOCHHMM MODEL FILE

<MODEL INFORMATION>
======================================================
MODEL_NAME:	GC Model
MODEL_DESCRIPTION:	Taken from Problem 3.16 from Problems and Solutions in Biological Sequence Analysis
MODEL_CREATION_DATE:	August 28,2009


<TRACK SYMBOL DEFINITIONS>
======================================================
TRACK1:	A,C,G,T

<STATE DEFINITIONS>
####################################################################################################
STATE:	
	NAME:	INIT
TRANSITION:	STANDARD:	P(X)
	H:	0.5
	L:	0.5

####################################################################################################
STATE:	
	NAME:	H
	GFF_DESC:	HIGH
	PATH_LABEL:	H
TRANSITION:	STANDARD:	P(X)
	H:	0.5
	L:	0.5
	END:	1
EMISSION:	TRACK1: P(X)
	ORDER:	0
0.2	0.3	0.3	0.2

####################################################################################################
STATE:
	NAME:	L
	GFF_DESC:	LOW
	PATH_LABEL:	L
TRANSITION:	STANDARD:	P(X)
	H:	0.4
	L:	0.6
	END:	1
EMISSION:	TRACK1: P(X)
	ORDER:	0
0.3	0.2	0.2	0.3

####################################################################################################
//END