Fig 8.

(a)Number of MBSs identified by each CSSM in the presence (AE) and absence (NF) of ΔG_open filtering. Values > 40 are excluded from the plot for comparative purposes. Red (upper) numbers and green (lower) numbers show the mean and the median respectively of the number of MBSs identified by each CSSM. miRAW-Pita_AE and miRAW-TS_AE have the lowest number of MBSs while miRAW_6-1:10_AE has the highest. The number of sites discarded by accessibility energy filtering (AE) is higher in non-canonical oriented CSSMs than in canonical-oriented ones. (b) Relationship between the probability of miRAW obtaining a false positive prediction and the number of sites identified by each CSSM. The fact that miRAW classifies a miRNA:mRNA duplex as positive if a single miRNA:MBSs is predicted as positive by the neural network increases the chances of obtaining a false-positive prediction as the number of potential MBSs increases. As non-canonical oriented CSSMs tend to detect higher numbers of potential MBSs they are more sensitive to a false positive. The application of ΔG_open filtering reduces the number of potential MBSs and therefore reduces the probability of a false positive.