RNAstructure Command Line Help |
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PARTS takes two homologous sequences as input and aligns the two sequences and predits base pairing probabilities for conserved structures. It can run in three modes: map (maximum a posteriori) mode to find a maximum probability structure, pp (pair probability) mode, which yields a matrix of base pairing probabilities, or stochsample (stochastic sampling) to sample generated structures. USAGE: PARTS <configuration file>Required parameters:
Options that do not require added values:NONEOptions that require added values:NONEConfiguration file format:The following is a description of valid options allowed in the configuration file. ################################################################ # IMPORTANT CONFIG FILE FORMAT NOTES: # # Config file options described below are case sensitive. # # Option lines may be specified by the option name followed by a space and the option's desired value. # When specifying an option, there may be nothing else on the line. # <option> <value> # # Specifying comment lines: # Comment lines must begin with "#" followed by a space. # There may not be more than one "#" in a comment line. # However, a comment line may be an unbroken string of "#", as in a divider between sets of options. # # Blank lines are skipped. ################################################################ ################################################################ # Required input ################################################################ seq1 seq1.seq seq2 seq2.seq mode map (or pp or stochsample) ################################################################ # Output files; if these aren't specified defaults are used. ################################################################ # Output file for sequence 1 in pp mode seq1_pp_op ../my_pp1 # Output file for sequence 2 in pp mode seq2_pp_op my_pp2 # Output ct for sequence 1 in stochsample mode seq1_sample_ct_op ../my_ct1_sample.txt # Output ct for sequence 2 in stochsample mode seq2_sample_ct_op ../../my_ct2_sample.txt # Output alignment file for stochsample mode sample_aln_op ./my_aln_sample.txt # Output ct for sequence 1 in map mode seq1_map_ct_op ../my_map_ct1.txt # Output ct for sequence 2 in map mode seq2_map_ct_op ../../my_map_ct2.txt # Output alignment file for map mode map_aln_op ../my_map_aln.txt ################################################################ # Other parameters ################################################################ # Number of structures to sample in stochsample mode nsamp 1000 References:
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