miRNA target recognition using features of suboptimal alignments

MicroRNAs (miRNAs) are a class of short RNA molecules that regulate gene expression by binding directly to messenger RNAs. Conventional approaches to miRNA target prediction estimate the accessibility of target sites and the strength of the binding miRNA by finding optimums of some energy models, which involves O(n3) computations. Alternatively, we narrow down potential binding sites of miRNAs to suboptimal hits of a pairwise alignment algorithm called Fitting Alignment in O(n2). We invoke a same algorithm, once for all candidate sites to measure the site accessibilities. These features are applied to a binary classifier being learned to predict true associations between miRNAs and target genes. Training the classifier requires the negative samples indicating non-affected genes. The experiments verifying such negative associations have been rarely performed, so we exploit tissue-specific gene expression data to impute the negative associations. The recall rate of our method is above 70% (at precision 85%).