lottpaul edited this page Jan 23, 2013
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##CpG Model
[Borodovsky, M., Ekisheva, S., Problems and Solutions in Biological Sequence Analysis. Cambride University Press, 2006, pg 80]
##Model File
#STOCHHMM MODEL FILE
<MODEL INFORMATION>
======================================================
MODEL_NAME: CpG
MODEL_DESCRIPTION: Taken from CH3 Durbin/Eddy 3.16, 3.17
MODEL_CREATION_DATE: August 28,2009
<TRACK SYMBOL DEFINITIONS>
======================================================
TRACK1: A,C,G,T
<STATE DEFINITIONS>
######################################################
STATE:
NAME: INIT
TRANSITION: STANDARD: P(X)
HIGH: 0.5
LOW: 0.5
####################################################
STATE:
NAME: HIGH
GFF_DESC: HIGH
PATH_LABEL: H
TRANSITION: STANDARD: P(X)
HIGH: 0.5
LOW: 0.5
END: 1
EMISSION: TRACK1: P(X)
ORDER: 0
0.2 0.3 0.3 0.2
###################################################
STATE:
NAME: LOW
GFF_DESC: LOW
PATH_LABEL: L
TRANSITION: STANDARD: P(X)
HIGH: 0.4
LOW: 0.6
END: 1
EMISSION: TRACK1: P(X)
ORDER: 0
0.3 0.2 0.2 0.3
##################################################
//END
##Sequence File
>Example 3.16 Example
GGCACTGAA