Algorithm for thermodynamically based prediction of DNA/DNA cross-hybridisation

Authors:
Svetlana Torgasin;Karl-Heinz Zimmermann
Affiliations:
Department of Computer Engineering, Hamburg University of Technology, 21071 Hamburg, Germany.;Department of Computer Engineering, Hamburg University of Technology, 21071 Hamburg, Germany
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2010

Citing 7
Cited 0

Molecular computation of solutions to combinatorial problems

Science
Internal loops in RNA secondary structure prediction

RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Dynamic Programming

Dynamic Programming
A fractional programming approach to efficient DNA melting temperature calculation

Bioinformatics
Efficient identification of DNA hybridization partners in a sequence database

Bioinformatics
Effective heuristic methods of dna strand design

Effective heuristic methods of dna strand design
DNA Computing Models

DNA Computing Models

Quantified Score

Hi-index	0.00

Visualization

Abstract

A careful design of DNA strands is crucial for several biological applications such as microarray techniques, Polymerase Chain Reaction (PCR), and DNA computing. For this, the important criterion under laboratory conditions is the hybridisation energy of two DNA strands. During the last decade, a thermodynamic model was developed that allows for the calculation of the DNA/DNA hybridisation energy and recently also the cross-hybridisation energy of structural motifs. Employing this model a new algorithm for the secondary structure prediction of DNA/DNA cross-hybridisation complexes called HYBGRAPH is introduced. The method is based on Gibbs free energy minimisation and the paradigm of dynamic programming.