KnotInFrame: prediction of -1 ribosomal frameshift events

Theis, Corinna; Reeder, Jens; Giegerich, Robert

The dominance of is_m_is_is3 is undefined ('b' in Table 2 ) since the slippery site is out of KnotInFrames scope due to the remarkable appearance of the slippery sequence: it has a length of only 4 nt. The À1 PRF signal of pol_m_vir_gill has a total length of 177 nt but the longest substring the pipeline folds is 120 nt. A more detailed look at the annotation, reveals that the classification as a pseudoknot is at least questionable: the À1 PRF pseudoknot signal has been predicted by a hairpin folding via Mfold. Afterwards, the hairpin has been manually extended to a pseudoknot, by looking downstream for a complementary site which is able to pair with the hairpin loop region. This is also the reason for the exceptional length of the structure. An examination of the second stem with RNAduplex from the Vienna RNA package revealed a free energy of only À5.7 kcal/mol. In accordance with the energy models implemented in state-ofthe-art pseudoknot folding programs, this energy might be too low to compensate for the destabilizing effects of the pseudoknot loops. A similar consideration holds for the entry of pol_m_ vir_hcv. Its annotated pseudoknot is much longer than the maximal length of our consensus model. In this case, our pipeline folds at most the first 120 nt of the whole structure and hence can only find an alternative, suboptimal pseudoknot. Thus, this site is ranked low in our evaluation. A possible reason for predicting the frameshift signal of edr_m_euk_mmus on rank 5 might be that the structural frameshift component is not the pseudoknot reported in the RECODE. In (25) a more complicated pseudoknot with a 3 nt bulge in the first stem is reported. Our consensus model does not account for such pseudoknots and hence an alternative, suboptimal structure is folded. Consequently this structure is then ranked low by KnotInFrame.