Employing the tools ClustalW, RNAalifold, RNAfold and RNAforester, this pipeline can improve structural conservation of RNA sequences within the twilight zone of 30-60% sequence identity. After constructing a consensus structure by alignment folding, plan AC* abandons the original sequence alignment, refolds structures individually, but restricted by the consensus, aligns the structures (irrespective of sequence) by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc...

• Perl Implementation of Plan AC*, needs BioPerl to be installed on your System.
• Usage: perl Pipeline.pl <FASTA-File> [-p=(0..9)] [-r=(0..2)] [-sci] (see README.txt)
• Please make sure to customise the configuration file - Pipeline.xml - before usage.