StochHMM File Formats

#5. File Formats

##5.2 Multiple Models File Format Models file contains complete path or relative path to multiple model files

#STOCHHMM MODELS
Model/GC_0_27/E1.hmm
Model/GC_22_32/E1.hmm
Model/GC_27_37/E1.hmm

##5.3 Model File Divider lines shown as “====” or “####” are optional, but you’re encouraged to use them to make the model easier to read.

###5.3.1 Model Header (Required) The first line of a model file must contain the header.

#STOCHHMM MODEL FILE

###5.3.2 Model Information (Optional) Each model can contain a name, description, creation date information, creation commands, author, numerical attribute or range.

If a numerical attribute is assigned, a model function

#STOCHHMM MODEL FILE

MODEL INFORMATION
================================================
NAME:	Simplified Human Gene
DESCRIPTION:	Created using perl script
CREATION_DATE:	August 12,2009
CREATION_COMMAND:	./creation_script.pl fasta.fa....
AUTHOR:	Paul Lott
NUM_ATTRIB:	20
UPPER:	29
LOWER:	20

NAME => Name of the model DESCRIPTION => Description of the model CREATION_DATE => Date that the model was created CREATION_COMMAND => Command or script used to create the model AUTHOR => Who created the model NUM_ATTRIB => Numerical value associated with the model. When using multiple models, StochHMM could select the model based on the value associated with the model. For example, if you have multiple models trained for sequences with different GC percentages. StochHMM could select the model based on the GC percentage of the sequence. UPPER => Range value, similar to NUM_ATTRIB except defines the inclusive upper range of values associated with the model. If used LOWER must also be supplied. LOWER => Range value, similar to NUM_ATTRIB except defines the inclusive lower range of values associated ith the model. If used UPPER must also be supplied.