miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs
Fig 2
Improved hairpin precursor Span identification.
a miRWoods generates several potential hairpin precursor spans from each product that passes through the MPRF. Duplex-focused spans take the region between the product and the optimal duplex and product-focused spans take the region between the product and other products greater than 4 nt away. Hairpins are selected based on HPRF score. b The miRBase annotation for hsa-mir-4721 crosses over an intron boundary. miRWoods corrects the annotation by recognizing a second read stack and produce precursor span that perfectly matches an intron, suggesting mir-4721 is a mirtron. c The miRWoods prediction for mmu-let-7c-2 in mouse is consistent with the miRBase annotation, while the best miRDeep2 prediction, albeit below the default signal-to-noise threshold, only partially overlap with the miRBase annotation.