Refolding Individual Sequences

The refold.pl script removes gaps and maps the consensus structure to each individual sequence.

  $ RNAalifold  RNaseP.aln >  RNaseP.alifold
  $ gv alirna.ps
  $ refold.pl RNaseP.aln RNaseP.alifold | head -3 > RNaseP.cfold
  $ RNAfold -C --noLP < RNaseP.cfold > RNaseP.refold
  $ gv E-coli_ss.ps