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

Tagashira, M.; Asai, K.

doi:10.1101/812891

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bioRxiv · 10.1101/812891

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

Tagashira, M.·Asai, K.

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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.

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Tagashira, M., Asai, K.. 2019-10-21. RNAfamProb Plus NeoFold: Estimations of Posterior Probabilities on RNA Structural Alignment and RNA Secondary Structures with Incorporating Homologous-RNA Sequences. https://doi.org/10.1101/812891

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