considerations and rules for RNA folding
RNA folding and search software
- The UNAFold package: Prediction of hybridization, folding and melting profiles. N.R. Markham & M. Zuker.
mfold_util package for for creating structure and dot plots.
- Algorithms: Roumen Dimitrov, Nick Markham & Michael Zuker
- UNAFold: Nick Markham
mfold_util: Darrin Stewart & Michael Zuker; (porting and revisions by Nick Markham, Alex Yu and Michael Zuker)
- DINAMelt web server: Nick Markham; equipment donated by IBM Research
- Energy rules for RNA: Doug Turner, David Mathews et al.
- Energy rules for DNA: John SantaLucia et al.
- The DINAMelt web server for melting profile and Tm prediction.
- Download the
software. OligoArrayAux and mfold_util are also available
- The old Zuker-Turner RNA folding package.
- HMMER, Infernal and more: Software from the lab of Sean Eddy, HHMI, Janelia Farm Research Campus.
- The famous
Vienna RNA software package, by Ivo Hofacker,
Institut für theoretische Chemie, Vienna.
RNA secondary structure prediction server at the
Belozersky Institute of
physico-chemical biology at Moscow State University.
- The ESSA
package from the Département de Biométrie et Intelligence Artificielle,
- RNAdraw - by Ole Matzura (see below)
- Bruce Shapiro's STRUCTURELAB at the NIH.
3D RNA modeling & databases
RNA secondary structure display software
An interactive program by Darrin Stewart and Michael Zuker
for Unix/Linux computers (includes Mac OS X).
Part of the
mfold_util software package.
High quality images/interactive program
Bryn Weiser and Harry Noller at UC Santa Cruz.
- RNA Movies: Visualising RNA Secondary Structure Spaces.
Created by the Technische Fakultät group at University of Bielefeld.
SStructView: RNA Secondary Structure Java Applet
Helix Group at Stanford University.
A windows-type program for producing secondary structure drawings of RNA molecules.
by Peter De Rijk and Rupert De Wachter
The Rnadraw Homepage (from Sweden). Author is
Secondary Structures & Databases
The RNA World at IMB Jena
- Image Library of Biological Macromolecules
- Software and many other RNA links
Computational RNA Research at the NIH
Rensselaer Polytechnic Institute
Last Update: 5/19/08