3 # Last changed Time-stamp: <2005-03-09 19:38:25 ivo>
4 # produce Pauline's mountain representation from bracket notation
5 # use e.g. as RNAfold < foo.seq | b2mt | xmgr -pipe
6 # definition: h=number of base pairs enclosing base
11 next unless (/\.\.\./);
12 next if (/\[/); # don't process output from partition function
19 printf("%4d %4d\n",$p,$h);
20 $h++ if ($i eq '('); # increase $h *after* printing
27 b2mt - produce coordinates for a mountain plot from bracket notation
31 b2mt.pl < seq.fold > mountain.dat
35 read a secondary structures in bracket notation as output by RNAfold,
36 and compute coordinates for a mountain plot as introduced by Pauline Hogeweg.
37 The output is suitable for graphing with xmgrace, e.g.:
38 C< RNAfold < foo.seq | b2mt.pl | xmgrace -pipe>
42 Ivo L. Hofacker <ivo@tbi.univie.ac.at>