RNAfamProb Plus NeoFold: Estimations of Posterior Probabilities on RNA Structural Alignment and RNA Secondary Structures with Incorporating Homologous-RNA Sequences

Abstract

MotivationThe simultaneous optimization of the sequence alignment and secondary structures among RNAs, structural alignment, has been required for the more appropriate comparison of functional ncRNAs than sequence alignment. Pseudo-probabilities given RNA sequences on structural alignment have been desired for more-accurate secondary structures, sequence alignments, consensus secondary structures, and structural alignments. However, any algorithms have not been proposed for these pseudo-probabilities.\n\nResultsWe invented the RNAfamProb algorithm, an algorithm for estimating these pseudo-probabilities. We performed the application of these pseudo-probabilities to two biological problems, the visualization with these pseudo-probabilities and maximum-expected-accuracy secondary-structure (estimation). The RNAfamProb program, an implementation of this algorithm, plus the NeoFold program, a maximum-expected-accuracy secondary-structure program with these pseudo-probabilities, demonstrated prediction accuracy better than three state-of-the-art programs of maximum-expected-accuracy secondary-structure while demanding running time far longer than these three programs as expected due to the intrinsic serious problem-complexity of structural alignment compared with independent secondary structure and sequence alignment. Both the RNAfamProb and NeoFold programs estimate matters more accurately with incorporating homologous-RNA sequences.\n\nAvailabilityThe source code of each of these two programs is available on each of \"https://github.com/heartsh/rnafamprob\" and \"https://github.com/heartsh/neofold\".\n\nContact\"tagashira_masaki_17@stu-cbms.k.u-tokyo.ac.jp\" and \"asai@k.u-tokyo.ac.jp\".\n\nSupplementary informationSupplementary data are available at Bioinformatics online.