refold.pl − refold using consensus structure as constraint
refold.pl [−t thresh] file.aln alidot.ps refold.pl [−−turn length] file.aln file.alifold
refold.pl reads an alignment in CLUSTAL format, and a consensus secondary structure, either in the form of the standard output of "RNAalifold", or in the form of a dot plot as produced by "RNAalifold −p". For each sequence in the alignment it writes the name, sequence, and constraint structure to stdout in a format suitable for piping into "RNAfold −C".
The constraint string is produced by removing from the consensus structure all gaps, as well as all pairs not compatible with the particular sequence. If the structure is read from a dot plot file, only pairs with probability > then some threshold (default 0.9) are used.
use only pairs with p>thresh as constraint. Only applicable when reading consensus structure from a dot plot.
use only pairs closing a hairpin with looplength >length. This option allows for setting minimal loop length of hairpin loops (default: 3)
RNAalifold test.aln > test.alifold refold.pl test.aln test.alifold > test.cfold RNAfold −C < test.cfold