Kisses, ambivalent models and more: Contributions to the analysis of RNA secondary structure

Keywords

Protein secondary structure, Nucleic acid secondary structure, RNA, Computer science, Dynamic programming

References

• UNAFold: software for nucleic acid folding and hybridization.好 廿日出, 伸也 奥野, 三郎 田中 — 2008
• Compiling a domain specific language for dynamic programmingSteffen Peter — 2006
• Bellman's GAP: a 2nd generation language and system for algebraic dynamic programmingGeorg Sauthoff — 2010
• Fast folding and comparison of RNA secondary structuresIvo L. Hofacker, Walter Fontana, Peter F. Stadler — 1994
• Complete probabilistic analysis of RNA shapesBjörn Voß, Robert Giegerich, Marc Rehmsmeier — 2006
• A comprehensive comparison of comparative RNA structure prediction approachesPaul P. Gardner, Robert Giegerich — 2004
• Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegansAndrew Fire, Siqun Xu, Mary K. Montgomery — 1998
• Versatile and declarative dynamic programming using pair algebrasSteffen Peter, Robert Giegerich — 2005
• PseudoBase: structural information on RNA pseudoknotsF. H. D. van Batenburg — 2001
• Effective ambiguity checking in biosequence analysisJanina Reeder, Steffen Peter, Robert Giegerich — 2005
• Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure predictionRobin D. Dowell, Sean R. Eddy — 2004
• The dynamic structural basis of differential enhancement of conformational stability by 5'- and 3'-dangling ends in RNA.John D. Liu, Liang Zhao, Tianbing Xia — 2008
• Characterization of a "kissing" hairpin complex derived from the human immunodeficiency virus genome.Kung‐Yao Chang, I Tinoco — 1994
• Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs.Mark E. Burkard, Ryszard Kierzek, Douglas H. Turner — 1999
• Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolutionKevin A. Wilkinson, Edward J. Merino, Kevin M. Weeks — 2006
• Abstract shapes of RNA.Robert Giegerich — 2004
• Applications of stochastic context-free grammars using the Inside-Outside algorithmKimia Bazargan Lari, S. Young — 1990
• Efficient parameter estimation for RNA secondary structure predictionMirela Andronescu, Anne Condon, Holger H. Hoos — 2007
• The equilibrium partition function and base pair binding probabilities for RNA secondary structureJohn S. McCaskill — 1990
• A discipline of dynamic programming over sequence dataRobert Giegerich, Carsten Meyer, Steffen Peter — 2004

Cited by

• Algebraic Dynamic Programming over general data structuresChristian Höner zu Siederdissen, Sonja J. Prohaska, Peter F. Stadler — 2015
• Advances in Bioinformatics and Computational BiologySérgio Campos — 2014
• Dynamic Programming for Set Data TypesC. H. Z. Siederdissen, Sonja J. Prohaska, P. Stadler — 2014

Related papers

• EternaBrain: Automated RNA design through move sets from an Internet-scale RNA videogameRohan V. Koodli, Benjamin Keep, Katherine R. Coppess — 2018
• EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogameRohan V. Koodli, Benjamin Keep, Katherine R. Coppess — 2019
• A modularized MapReduce framework to support RNA secondary structure prediction and analysis workflowsBoyu Zhang, Daniel T. Yehdego, Kyle Johnson — 2012
• Application of high performance compute technology in bioinformaticsSven Warris — 2019
• Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequencesBin Liu, Fule Liu, Xiaolong Wang — 2015
• Developing and Applying Heterogeneous Phylogenetic Models with XRateOscar Westesson, Ian Holmes — 2012
• Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignmentD. Sundfeld, Jakob H. Havgaard, Alba Cristina Magalhães Alves de Melo — 2015
• Succinct data structures for assembling large genomesThomas Conway, Andrew Bromage — 2010
• Applications of a generic model of genomic variations functional analysisSarah N. Mapelli, Uberto Pozzoli — 2012