Next: COMMAND LINE PARAMETERS Up: Algorithms and Thermodynamics for Previous: Constrained folding

Running the programs

The main program in the mfold package is named mfold . It is really a (Unix shell) script that calls a number of Fortran and C programs and puts together a reasonable output. Calling the mfold script without any command line parameters will cause the following output:

Usage is
mfold SEQ=`file_name' with optional parameters:
[ AUX=`auxfile_name' ] [ RUN_TYPE=text (default) or html ]
[ NA=RNA (default) or DNA ] [ LC=sequence type (default = linear) ]
[ T=temperature (default = 37˚) ] [ P=percent (default = 5) ]
[ W=window parameter (default - set by sequence length) ]
[ MAXBP=max base pair distance (default - no limit) ]
[ MAX=maximum number of foldings to be computed (default 100) ]
[ ANN=structure annotation (default = none, p-num or ss-count) ]
[ START=5' base # (default = 1)] [ STOP=3' base # (default = end) ]
[ REUSE=NO/YES (default=NO) reuse existing .sav file ]

The meaning and use of these parameters are discussed below.

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• COMMAND LINE PARAMETERS
• OUTPUT
  • The energy dot plot
  • Optimal and suboptimal foldings
• AUXILIARY AND INDIVIDUAL PROGRAMS

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Michael Zuker Center for Computational Biology Washington University in St. Louis 1998-12-05