TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

(2016) Lei Hua et al.   PLoS One

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

(2015) Sebastian Will et al.   BIOINFORMATICS

Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures

(2015) Yinghan Fu et al.   PLoS One

Dynalign II: common secondary structure prediction for RNA homologs with domain insertions

(2014) Yinghan Fu et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation

(2013) Justin Ritz et al.   PLoS Computational Biology

TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots

(2012) Matthew G. Seetin et al.   BIOINFORMATICS

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

(2011) Arif O Harmanci et al.   BMC BIOINFORMATICS

Statistical evaluation of improvement in RNA secondary structure prediction

(2011) Zhenjiang Xu et al.   NUCLEIC ACIDS RESEARCH

Sequence embedding for fast construction of guide trees for multiple sequence alignment

(2010) Gordon Blackshields et al.   Algorithms for Molecular Biology

Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences

(2010) Zhenjiang Xu et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

ProbKnot: Fast prediction of RNA secondary structure including pseudoknots

(2010) S. Bellaousov et al.   RNA

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

(2009) Douglas H. Turner et al.   NUCLEIC ACIDS RESEARCH

Improved RNA secondary structure prediction by maximizing expected pair accuracy

(2009) Z. J. Lu et al.   RNA

A fast structural multiple alignment method for long RNA sequences

(2008) Yasuo Tabei et al.   BMC BIOINFORMATICS

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

(2008) Kazutaka Katoh et al.   BMC BIOINFORMATICS

RNAalifold: improved consensus structure prediction for RNA alignments

(2008) Stephan H Bernhart et al.   BMC BIOINFORMATICS

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

(2008) Arif Ozgun Harmanci et al.   NUCLEIC ACIDS RESEARCH

R-Coffee: a method for multiple alignment of non-coding RNA

(2008) A. Wilm et al.   NUCLEIC ACIDS RESEARCH

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

(2008) F. Juhling et al.   NUCLEIC ACIDS RESEARCH