RNA structure prediction using positive and negative evolutionary information
Fig 3
The CaCoFold algorithm applied to the transfer-messenger RNA (tmRNA).
Steps (a) to (f) refer to the same methods as described in Fig 1. (a) Characteristics of the input alignment. (b) The statistical test that considers all possible pairs equally resulting in the assignment of 121 significantly covarying positive basepairs. The Rfam consensus structure in not used in the analysis. The whole analysis is performed using the single command R-scape --fold on the input alignment. The analysis takes 25 seconds (30s including drawing all the figures) on a 3.3 GHz Intel Core i7 MacBook Pro. (c) The maxCov algorithm requires 6 layers to incorporate all 121 positive basepairs. (d) The cascade Constraint folding completes the structure with a total of 139 basepairs. (e) After filtering, there are five pseudoknoted helices, three triplets and 10 other mRNA-induced covariations. The structural display in (f) has been modified by hand to match the standard depiction of the tmRNA secondary structure in (g). The thick line in (g) marked with an asterisk indicates the C-C triplet interaction proposed in Ref. 44. Details of the mRNA-induced covariations are given in S6(c) Fig.