Functional options:
-I: integrate .ptt and .rnt file into .ano file;
Necessary inputs: -p, -r and -o;
-T: scoring schemes calculated by EM algorithm:
Necessary inputs: -n, -o, -t and -s.
-S: scanning for sigma factor binding sites
Necessary inputs: -n, -o, -f, -p (or -a), -w and -h
Optional inputs: -l, -g, -u and -c.
Parameters for inputs:
Inputs with no default value:
-n NC number (eg: NC_000913)
-o output directory
-f .fna file directory
-a .ano file directory
-p .ptt file directory
-r .rnt file directory
-h threshold input file directory
-t Training set sequences directory
-w parameters of scoring scheme file directory
-s file that include sigma factor parameters for position weight matrix
Attention: the file name of these inputs are not required!
Inputs with default value:
-l threshold of intergenic distance (default value is 100)
-g region length for promoter scanning (default value is 250)
-u the chosen number of PWM calculated by user
if nothing is inputted, the program will utilize the default PWMs,
otherwise four inputted numbers should be seperated by blanks (eg: 1 2 5 26)
-c the sigma promoters excluded from scanning"
if nothing is inputted, the program will scan for all four sigma promoters,
otherwise inputted sigma promoters should be seperated by blanks (eg: Sigma38 Sigma32 Sigma24).
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