REPEATS, SECONDARY STRUCTURE & MELTING TEMPERATURE

REPEATS, SECONDARY STRUCTURE

DNA often contains reiterated sequences of differing length. These include direct (e.g. GAAT-N6-GAAT) and inverted (GAAT-N6-ATTC) repeats. The later, if sufficiently close may form stable stem-loop structures.  For secondary structures of RNA or DNA I recommend most highly Michael Zuker’s sites:

For RNA folding use MFold (Michael Zuker, Rensselaer Polytechnic Institute, U.S.A.).  N.B. The data can be presented in a number of graphic formats. For DNA sequences use this site. 
Vienna RNA secondary structure prediction  (University of Vienna, Austria). I have found this site useful for drawing tRNAs in cloverleaf format.
pknotsRG (Universität Bielefeld, Germany) - is a series of 3 tools for folding RNA secondary structures, including the class of simple recursive pseudoknots. Unfortunately to optimally view the results one needs Microsoft.NET framework (massive) and PseudoViewer2 (School of Computer Science and Engineering, Inha University, Korea).

REPuter - fast computation of maximal repeats in complete genomes (S. Kurtz & C. Scheiermacher @ Universitat Bielefeld, Germany) - interesting graphical representation of repeats.
REPFIND (ZLAB,  Dr. Zhiping Weng, Boston University, U.S.A.) - on sequences of less than 20kb it provides graphical and statistical analysis on direct repeats.
 einverted,  palindrome and equicktandem - (EMBOSS) - find inverted and tandem repeats

 CRISPRfinder  Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) present a curious repeat structure found in many prokaryotic genomes. They show characteristics of both tandem and interspaced repeats. (Reference: I. Grissa et al. 2007. Nucl. Acids Res. 35(Web Server issue): W52-W57).

For those with a fuller knowledge of DNA secondary structure you might want to visit ICGEB: International Centre for Genetic Engineering and Biotechnology (Italy)

bend.it and plot.it

model-it - (K. Vlahovicek & S. Pongor) produces incredible pictures of DNA using a variety of parameters. Right click on screen to download the picture, which may not be visible. N.B. you will require Rasmol to visualize the results (*.pdb file).
Sequence-Directed DNA Curvature Wedge Model Formalism and DNA Path Computation (Haifa Genome Diversity Center, University of Haifa, Israel) - this site also gives an elegant output which requires a VRML plug-in and converter for  visualizing and manipulating the results.  I found that Internet Explorer worked best.
DNAcurve - (D. Wheeler, Marine Biological Laboratory, U.S.A.) also analyzes DNA for curvature using a dinucleotide wedge model. The diagrams are not as high quality.  Appears to work best with Netscape.

MELTING TEMPERATURE

Knowing the melting temperature of a fragment of DNA or of an oligonucleotide is invaluable in the determining optimal conditions for carrying out hybridizations.  All of the PCR design sites will provide information on oligonucleotides the following will accommodate longer sequences:

Poland service request form (Heinrich Heine-Universität Düsseldorf, Germany). Please note, in Netscape hit the "stop" button to turn off the animation which may interfere with your ability to use this site.
DAN (Le Centre de Bioinformatique de Bordeaux, France ) - provides one with a plot (in postscript).   For a complete picture of your sequence change "window size" to the size of your fragment, change "shift increment" to zero, and click on "Produce a plot".

Hybridization of two different strands of DNA or RNA - Computations consider 5 different ensembles of structures. Partition function calculations are performed for the heterodimer, the two possible homodimers, and for folding of both single strand. Ensemble free energies are computed, leading to simulation of heat capacity, Cp, as a function of temperature. Base pair probabilities are computed and combined with published extinction coefficients to simulate UV absorbance as a function of temperature. (Reference: N.R. Markham & M. Zuker 2005.  Nucl. Acids Res. 33: W577-W581).

Homodimer simulations - This simulation considers both the folding and dimerization of one single-stranded DNA or RNA molecule. (Reference: N.R. Markham & M. Zuker 2005.  Nucl. Acids Res. 33: W577-W581).