Figure 2: Efficiency of filtering steps and paired HMM. Receiver operating characteristic (ROC) curves for filters on (a) minimum length of stem-loop region, (b) fraction of base pairs in a sliding window of 25 states, (c) number of consecutive base pairs, and (d) ratio of sequence and stem-loop length. The area under the curve (AUC) is (a) 0.94, (b) 0.97, (c) 0.93, and (d) 0.87. The dots (at m a x ( s e n s i t i v i t y + s p e c i c i t y 1 ) ) denote the value pair of sensitivity and false positive rate that optimally discriminates between miRNA and non-miRNA sequences. The data set consisted of all plant miRNA sequences from MIRBASE 10 and 455 non-miRNA sequences from RFAM 7.