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Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization and experimental constraints, derived from enzymatic and flavin mononucleotide cleavage, improve the accuracy of structure predictions.
RNAstructure: software for RNA secondary structure prediction and analysis
New extensions to RNAstructure are described, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces that serve to make RNA secondary structure prediction user- friendly.
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
- D. Mathews, M. Disney, Jessica L Childs, S. Schroeder, M. Zuker, D. Turner
- ChemistryProceedings of the National Academy of Sciences…
- 11 May 2004
A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments…
Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
The details of the free energy rules and of the latest version 3.0 software are described and future plans are also discussed.
Accurate SHAPE-directed RNA structure determination
- Katherine E Deigan, Tian W Li, D. Mathews, K. Weeks
- BiologyProceedings of the National Academy of Sciences
- 6 January 2009
It is demonstrated that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy, comparable to the best accuracies achievable by comparative sequence analysis.
High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States
High-throughput SHAPE technology is invented, which uses many of the same tools as DNA sequencing to quantify RNA backbone flexibility at single-nucleotide resolution and reveals a comprehensive view of HIV-1 RNA genome structure, and further application will make possible newly informative analysis of any RNA in a cellular transcriptome.
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.
- A. E. Walter, D. Turner, M. Zuker
- Biology, ChemistryProceedings of the National Academy of Sciences…
- 27 September 1994
An RNA model system consisting of an oligomer binding to a 4-nt overhang at the 5' end of a hairpin stem provides thermodynamic parameters for helix-helix interfaces and predictions of 11 RNA secondary structures improve from 67 to 74% accuracy by inclusion of similar stacking contributions.
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
The Nearest Neighbor Database (NNDB, http://rna.urmc.rochester.edu/NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each…
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.
Dynalign is a new computer algorithm that improves the accuracy of structure prediction by combining free energy minimization and comparative sequence analysis to find a low free energy structure common to two sequences without requiring any sequence identity.
RNAstructure: web servers for RNA secondary structure prediction and analysis
- Stanislav Bellaousov, Jessica S. Reuter, M. Seetin, D. Mathews
- BiologyNucleic Acids Res.
- 24 April 2013
The web server offers RNA secondary structure prediction, including free energy minimization, maximum expected accuracy structure prediction and pseudoknot prediction, and can predict secondary structures conserved in either two homologicals or more than two homologs.