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.

SStructView - (Found July 2, 2008 )

RNA secondary structure viewer applet; must be integrated into web page to be implemented; can link to multiple computational backends.
http://smi-web.stanford.edu/projects/helix/sstructview/

taveRNA - (Found July 2, 2008 )

taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.
http://compbio.cs.sfu.ca/taverna/

ProMiR II - (Found July 2, 2008 )

Probabilistic miRNA prediction (ProMiR) is a resource that includes: ProMiR-v to search for both conserved and non-conserved miRNAs in the vicinity of a known miRNA; ProMiR-c to predict both conserved and non-conserved miRNAs in the vicinity of a candidate (70150 nt); and ProMiR-g to predict miRNA genes in a long sequence (70 nt10 kb) of various speceis.
http://cbit.snu.ac.kr/~ProMiR2/

pknotsRG - (Found July 2, 2008 )

pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.
http://bibiserv.techfak.uni-bielefeld.de/pknotsrg/

CARNAC - (Found July 2, 2008 )

Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.
http://bioinfo.lifl.fr/carnac

CorreLogo - (Found July 2, 2008 )

CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated.
http://correlogo.abcc.ncifcrf.gov/

GPRM - (Found July 2, 2008 )

Genetic Programming for RNA Motifs (GPRM) finds common secondary structure elements in a set of unaligned RNA sequences.
http://bioinfo.cis.nctu.edu.tw/service/gprm/

ILM - (Found July 2, 2008 )

Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences.
http://cic.cs.wustl.edu/RNA/

INFO-RNA - (Found July 2, 2008 )

INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.
http://www.bioinf.uni-freiburg.de/Software/INFO-RNA/start.html

Kinefold - (Found July 2, 2008 )

Kinefold calculates (and animates) the folding kinetics of RNA sequences including pseudoknots.
http://kinefold.u-strasbg.fr/