KnotInFrame: prediction of -1 ribosomal frameshift events

Theis, Corinna; Reeder, Jens; Giegerich, Robert

S. cerevisiae (5) . It is based on a two-step procedure, where the first step identifies slippery sequences followed by a possible frameshift pseudoknot. In the second step, candidates are analyzed statistically. In more detail, RNAmotif (12) is used in the first step and finds all potential pseudoknots that could be formed according to a descriptor. The descriptor specifies the allowed loop and helix lengths which are extracted from known À1 PRF pseudoknots. All potential pseudoknots are then subjects of statistical analysis in step two. The potential pseudoknots are refolded with pknots (13), a minimum free energy (MFE)-based RNA folding algorithm, capable of predicting a wide class of pseudoknots. The MFE of the folding is compared to folding energies of randomized sequences via z-score analysis. Finally, sequences with a low z-score (<À1.65) are regarded as statistically significant, since they appear to be more stable than expected by random.