Mfold manual

The command syntax is rigid. The various commands and syntax are given below. Next: Running the programs Up: Algorithms and Thermodynamics for Previous: Loops and Nearest neighbor Constrained folding In addition to the free energy rules, specific constraints may be used to force or prohibit base pairs. Forcing a string of consecutive bases to pair. Syntax: F i 0 k Ribonucleotides are forced to be double stranded. The partners for these bases are chosen by the program.

As an example, the command: F 23 0 5 would cause bases 23, 24, 25, 26 and 27 to pair. Forcing a string of consecutive base pairs. Syntax: F i j k Base pairs are forced to occur. This is the same thing as forcing a helix to form. ANN' : This file contains P-num information for a particular. The i th record contains i and. This file is used for annotating plotted structures.

These files are usually sorted by h-num; lowest to highest, or best determined to worst determined. Often, only helices in optimal foldings are retained. Figure 10 shows part of a sorted and filtered h-num file corresponding to the plot file in Figure 9. Figure 9: Selected records from a plot file. Note that this is not the free energy of the helix, but the mimimum free energy of any folding that contains the helix.

Up to version 2. Versions 2. The RNA folding web server at mfold. This server will be described elsewhere. It's main advantage is that anyone with a web browser can use it.