Structure Prediction

Great number of softwares have been dedicated to this category but still secondary structure prediction is a hard problem. Traditional softwares such as mfold and RNAfold use dynamic programming based on free energy minimization. Recent methods incorporate multiple sequence alignment into secondary structure prediction, which greatly helps eliminating unconserved structure.

Pseudoknot — by admin — last modified 2006-10-27 22:25

Pseudoknot-aware prediction tools are starting to appear recently, as if it represents the increasing demands for such tools since newly discovered RNAs have pseudoknots these days. The problem is its computational complexity.

Tertiary Structure Prediction — by admin — last modified 2006-10-27 22:25

 

mfold — by admin — last modified 2006-10-27 22:25

mfold is the standard implementation of dynamic programming algorithm for RNA secondary structure prediction developed by Prof. Michael Zuker. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (13), 3406-15, (2003)

Vienna RNA Package — by admin — last modified 2006-10-27 22:25

A famous software package of many standalone RNA softwares and library. RNAfold is for secondary structure prediction based on minimum free energy and RNAsubopt is for sub-optimal secondary structure prediction. RNAaliforld if for common secondary structure prediction from multiple sequence alignment.

Pfold — by admin — last modified 2006-10-27 22:25

Highly accurate secondary structure prediction software based on SCFG. Pfold accepts multiple sequence alignment information as its input. Its grammar is usually refered as KH-99 after its authors Knudsen and Hein. KH-99 is efficient and simple grammar. Currently, web service only.

BayesFold — by admin — last modified 2006-10-27 22:25

BayesFold is a web application that finds, ranks, and draws the likeliest structures for a sequence alignment. Foldings are based on the predictions of the Bayesian statistical method. BayesFold provides convenient structure comparison and formatting functionality, and produces publication-quality graphics.

RNA & DNA Folding Applications — by admin — last modified 2006-10-27 22:25

The Rensselaer and Wadsworth bioinformatics web server provides wide range of RNA-related applications. Michael Zuker's mfold is available on this server while many more new algorithms are also available.

Sfold — by admin — last modified 2006-10-27 22:25

Sfold is a set of "Software for Statistical Folding and Rational Design of Nucleic Acids" where the nucleic acids mainly means siRNAs. Sfold is developed and provided by Y. Ding et al. on Rensselaer and Wadsworth Bioinformatics Web Server.

RNAshapes — by admin — last modified 2006-10-27 22:25

RNAshapes predicts most probable representative "shapes" (i.e. abstraction of secondary structure) from a RNA sequence. More useful than Vienna's RNAsubopt because it effectively presents meaningful representative structures. Very fast.