RNALalifold

Calculates locally stable RNA secondary structure with a maximal base pair span. For a sequence of length n and a base pair span of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short RNA

Input format

RNALalifold requires one input file - Clustal file

Outputs

• energy of the consensus structures in the clustal file
• several possible postscript images bundled together in a tar file