Bioinformatics Links Directory : Structure Prediction, Visualization, and Design

Contains links to applications for the visualization, prediction, and design of RNA molecules including siRNAs, secondary structure, and folding kinetics.

ARTS - (Found July 2, 2008 )

Alignment of RNA Tertiary Structures (ARTS) is a method for aligning two nucleic acid structures (RNAs or DNAs) and detecting a-priori unknown common substructures.
http://bioinfo3d.cs.tau.ac.il/ARTS/

PSEUDOVIEWER - (Found July 2, 2008 )

PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.
http://wilab.inha.ac.kr/pseudoviewer2/

RNA Movies - (Found July 2, 2008 )

RNA Movies is a tool for the visualization of RNA secondary structure spaces. The program creates an interpolated animation of user provided sets of secondary structure data.
http://bibiserv.techfak.uni-bielefeld.de/rnamovies/

RNAbor - (Found July 2, 2008 )

RNAbor is a server for computing structural neighbors of a RNA secondary structure.
http://bioinformatics.bc.edu/clotelab/RNAbor/

RNAfold - (Found July 2, 2008 )

Predict RNA secondary structure from sequence; note sequence length limit.
http://www.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

RNALOSS - (Found July 2, 2008 )

RNALOSS (RNA locally optimal secondary structure) is a tool for the computation of locally optimal secondary structures.
http://bioinformatics.bc.edu/clotelab/RNALOSS/

RNAsoft - (Found July 2, 2008 )

Software for RNADNA secondary structure prediction and design
http://www.rnasoft.ca/

RNAz - (Found July 2, 2008 )

RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.
http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi

RSRE - (Found July 2, 2008 )

RNA Structural Robustness Evaluator (RSRE) is a tool for RNA structural robustness evaluation.
http://biosrv1.bmi.ac.cn/RSRE/

SEM - (Found July 2, 2008 )

Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization; some configuration necessary.
http://dicsoft2.physics.iisc.ernet.in/sem/