DMfold: A Novel Method to Predict RNA Secondary Structure With Pseudoknots Based on Deep Learning and Improved Base Pair Maximization Principle

Research on folding diversity in statistical learning methods for RNA secondary structure prediction

(2018) Yu Zhu et al.   International Journal of Biological Sciences

bpRNA: large-scale automated annotation and analysis of RNA secondary structure

(2018) Padideh Danaee et al.   NUCLEIC ACIDS RESEARCH

Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best

(2017) Max Ward et al.   NUCLEIC ACIDS RESEARCH

A semi-supervised learning approach for RNA secondary structure prediction

(2015) Haruka Yonemoto et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

C o F old : an RNA secondary structure prediction method that takes co-transcriptional folding into account

(2013) Jeff R. Proctor et al.   NUCLEIC ACIDS RESEARCH

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming

(2011) Kengo Sato et al.   BIOINFORMATICS

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

ConStruct: Improved construction of RNA consensus structures

(2008) Andreas Wilm et al.   BMC BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS