Bubblyhelix

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