Bubblyhelix is software for modeling the physics and thermodynamics of DNA.

The Bubblyhelix software was designed to work on large genomic DNA sequences, such as whole human chromosomes, using only a typical laptop or similar. The problem with large sequences is the limited amount of RAM memory. Bubblyhelix uses at most a few gigabytes RAM, without trade-offs in numerical or physical accuracy, it is a lossless algorithm.

Computations are done according to the thermodynamic model and algorithm described in the article:
E. Tøstesen, F. Liu, T.-K. Jenssen and E. Hovig (2003): Speed-up of DNA melting algorithm with complete nearest neighbor properties. Biopolymers, 70, 364-376.
The same model and algorithm is also used by the web-based tools at Stitchprofiles.uio.no.

Bubblyhelix is released under GPLv3.

Download the version 0.9.4 tarball here: bubblyhelix-0.9.4.tar.gz

Last update: Apr 2012

© 2012 Eivind Tøstesen