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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. Thermodynamic parameters for the stabilities of secondary structure motifsExpand
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RNAstructure: software for RNA secondary structure prediction and analysis
RNAstructure is a software package for RNA secondary structure prediction and analysis. Expand
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Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
This article is about the current status of the mfold package for RNA and DNA secondary structure prediction using nearest neighbor thermodynamic rules. Expand
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Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
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 incrementsExpand
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Accurate SHAPE-directed RNA structure determination
Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–functionExpand
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High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States
Replication and pathogenesis of the human immunodeficiency virus (HIV) is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We inventExpand
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Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.
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. In a sequence-dependent manner,Expand
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Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.
With the rapid increase in the size of the genome sequence database, computational analysis of RNA will become increasingly important in revealing structure-function relationships and potential drugExpand
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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. Expand
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Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented inExpand
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