Mfold

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You can read about the usage of the program in more detail at the 

Mfold web server page

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 deg C) ] [ P=percent (default = 5) ]
   [ NA_CONC=Na+ molar concentration (default = 1.0) ]
   [ MG_CONC=Mg++ molar concentration (default = 0.0) ]
   [ 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) ]
   [ MAX_LP=maximum bulge/interior loop size (default 30) ]
   [ MAX_AS=maximum asymmetry of a bulge/interior loop (default 30) ]
   [ ANN=structure annotation type: none (default), p-num or ss-count ]
   [ MODE=structure display mode: auto (default), bases or lines ]
   [ LAB_FR=base numbering frequency ] [ ROT_ANG=structure rotation angle ]
   [ START=5' base # (default = 1)] [ STOP=3' base # (default = end) ]
   [ REUSE=NO/YES (default=NO) reuse existing .sav file ]