A computer-assisted method for screening the relative activity of small catalytic RNAs is described. A series of four cis-acting variant sequence files are constructed based upon the RNA sequence of a trans-acting catalytic RNA under consideration. These files are individually folded into their lowest energy structure using a standard RNA folding algorithm. The compiled structures are assessed for their ability to form recognizable catalytic RNA secondary structure motifs. We demonstrate here that RNA sequences that do not readily fold into a cis-acting hammerhead ribozyme motif have trans-acting counterparts with reduced in vitro activity. This procedure should be useful in selecting the best candidate sequences in an mRNA to target for catalytic RNA cleavage.