RNA Structure

I. Structure Probing

1. Structure probing methods

关于RNA 二级结构高通量测序方法


2. Structure probing data analysis

  • 2021 Genome Biology - diffBUM-HMM a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data


II. Structure Motif Finder


1. Motif finding methods

  • 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

2. Applications

  • 2021 Science [TEISER] - A prometastatic splicing program regulated by SNRPA1 interactions with structured RNA elements

III. RNA Secondary Structure Prediction

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.