MFOLD 3.1.2 Prediction of RNA secondary structure M. Zuker M. Zuker, D.H. Mathews and D.H. Turner Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide in RNA Biochemistry and Biotechnology, J. Barciszewski and B.F.C. Clark, eds., NATO ASI Series, Kluwer Academic Publishers, (1999) mfold mfold perl "mfold RUN_TYPE=html" 0 SEQ Sequence File (SEQ) perl " SEQ=$value" 1 1 2 4 SEQ : The sequence file may contain multiple sequences. At present, the mfold script will fold the first sequence by default. LC Sequence type (default = linear) (LC) perl ($value and $value ne $vdef)?" LC=$value":"" linear 2 linear circular NA RNA (default) or DNA (NA) perl ($value and $value ne $vdef)?" NA=$value":"" RNA 2 RNA DNA control Control options 3 AUX Constraints File (AUX) perl " AUX=$value" 3 AUX : (optional) This is the name of an auxiliary input file of folding constraints. If this parameter is not used, mfold looks for a file named `fold_name.aux'. If this file exists and is not empty, then it is interpreted as a constraint file. Thus constraints may be used without the use of this command line parameter. Fill the box or the file with constraints (1 constraint per line) You may: 1. force bases i,i+1,...,i+k-1 to be double stranded by entering: F i 0 k 2. force consecutive base pairs i.j,i+1.j-1, ...,i+k-1.j-k+1 by entering: F i j k 3. force bases i,i+1,...,i+k-1 to be single stranded by entering: P i 0 k 4. prohibit the consecutive base pairs i.j,i+1.j-1, ...,i+k-1.j-k+1 by entering: P i j k 5. prohibit bases i to j from pairing with bases k to l by entering: P i-j k-l T Temperature (T) perl (defined $value and $value ne $vdef)?" T=$value":"" 37 3 P Percent (P) perl (defined $value and $value ne $vdef)?" P=$value":"" 5 3 P : This is the percent suboptimality for computing the energy dot plot and suboptimal foldings. The default value is 5%. This parameter controls the value of the free energy increment, delta (deltaG). Delta of deltaG is set to P% of deltaG, the computed minimum free energy. The energy dot plot shows only those base pairs that are in foldings with free energy minus or equal to deltaG plus delta (deltaG). Similarly, the free energies of computed foldings are in the range from deltaG to deltaG plus delta (deltaG). No matter the value of P, mfold currently keeps delta (deltaG) in the range [1,12] (kcal/mole). NA_CONC Na+ molar concentration (NA_CONC) perl (defined $value and $value ne $vdef)?" NA_CONC=$value":"" 1.0 3 MG_CONC Mg++ molar concentration (MG_CONC) perl (defined $value and $value ne $vdef)?" MG_CONC=$value":"" 0.0 3 W Window parameter (default - set by sequence length) (W) perl (defined $value)?" W=$value":"" 3 W : This is the window parameter that controls the number of foldings that are automatically computed by mfold . `W' may be thought of as a distance parameter. The distance between 2 base pairs, i.j and i'.j' may be defined as max{|i-i'|,|j-j'|}. Then if k-1 foldings have already been predicted by mfold , the kth folding will have at least W base pairs that are at least a distance W from any of the base pairs in the first k-1 foldings. As W increases, the number of predicted foldings decreases. If W is not specified, mfold selects a value by default based on sequence length, as displayed in Table 3. MAXBP MAXBP: Max base pair distance (default - no limit) perl ($value)?" MAXBP=$value":"" 3 MAXBP : A base pair i.j will not be allowed to form (in linear RNA) if j-i > MAXBP. For circular RNA, a base pair i.j cannot form if min{j-i,n+i-j} > MAXBP . Thus small values of MAXBP ensure that only short range base pairs will be predicted. By default, MAXBP=+infinity, indicating no constraint. MAX MAX: Maximum number of foldings to be computed perl ($value and $value ne $vdef)?" MAX=$value":"" 50 3 MAX : This is the maximum number of foldings that mfold will compute (50 by default). It is better to limit the number of foldings by careful selection of the P and W parameters. ANN Structure annotation type (default=none) (ANN) perl ($value and $value ne $vdef)?" ANN=$value":"" none 2 none p-num ss-count ANN : This parameter currently takes on 3 values. 1. `none' : secondary structures are drawn without any special annotation. Letters or outline are in black, while base pairs are red lines or dots for GC pairs and blue lines or dots for AU and GU pairs. 2. `p-num' : Colored dots, colored base characters or a combination are used to display in each folding how well-determined each base is according to the P-num values in the `fold_name.ann' file. 3. `ss-count' : Colored dots, colored base characters or a combination are used to display in each folding how likely a base is to be single-stranded according to sample statistics stored in the `fold_name.ss-count' file. Both 2. and 3. were recently described [38]. MODE Structure display mode (default=auto) (MODE) perl ($value and $value ne $vdef)?" MODE=$value":"" auto 2 auto bases lines ROT_ANG Structure rotation angle (ROT_ANG) perl ($value and $value ne $vdef)?" ROT_ANG=$value":"" 0 3 START 5' base number (START) perl ($value and $value ne $vdef)?" START=$value":"" 1 3 STOP 3' base number (default = end) (STOP) perl ($value)?" STOP=$value":"" 3 outfiles *.pnt *.plot *.ct *.html *.gif *.ps