HyTher – Software for hybridization kinetics of two NA pairs.
MARNA – is a multiple alignment of RNA s taking into consideration both the primary sequence and the secondary structure.
MFold – Zuker’s RNA folding algorithm
DINAmelt – Hybridization Applications for DNA & RNA The DINAMelt web server by Nick Markham & Michael Zuker
HCR Design – Pierce’s Hybridization design software.
Pseudoknot Design – Pierce’s partition function implementation for pseudoknots.
ViennaRNA – Command line automation of RNA design tools.
RNA Studio - A number of visualization tools including RNAMovie.
Nucleic Acid In Vitro Analsysis – A website for protocols on everything nucleic acid.
http://www.idtdna.com/SciTools/SciTools.aspx – A website to analize NA and calculate Extinction Coefficients
Software complied from Mathews and Turner. Cur Opin Struc Bio 2006 16:1-9.
RNAstructure – Using color annotation of base pair prob to determine base pairs predicted with high confidence
SFold – Secondary structure prediction by sampling
ILM - Iterated loop matching prediction of pseudoknots
HotKnots – Heuristic predction of pseudoknots
RNAcast – Determination of secondary structure common to two multiple sequences using abstract shapes
FOLDALIGN – Predction of RNA secondary structure common to two unaligned sequences
Dynalign – Predction of RNA secondary structure common to two unaligned sequences
RNAz – Discovery of ncRNA genes
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