2021 Genome Biology - diffBUM-HMM a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data
Graph Kernel: GraphProt - 2014 Genome Biology
SHAPE+HMM: PATTERNA - 2018 Genome Biology PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures
1994 Proc Int Conf Intell Syst Mol Biol Fitting a mixture model by expectation maximization to discover motifs in biopolymers
2005 NBT Assessing computational tools for the discovery of transcription factor binding sites
2006 Bioinformatics CMfinder: a covariance model based RNA motif finding algorithm
2008 Plos Computational Biology Discovering Sequence Motifs with Arbitrary Insertions and Deletions
2008 PNAS Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes
2014 Nature Method RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)
2015 Plos Computational Biology Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes
2021 Science [TEISER] - A prometastatic splicing program regulated by SNRPA1 interactions with structured RNA elements
RNAstructure/Mfold and RNAfold perform good for sequence less than 200nt.
SuperFold uses partition in RNAstructure package to predict partition functions for subsequences of long RNA, then merge the results. Therefore, it claims to perform better on long distance base pairs.
Deep Learning Method - see Deep Learning for RNA