Speed-Up of DNA Melting Algorithm with Complete Nearest Neighbor Properties

Details Speed-Up of DNA Melting Algorithm with Complete Nearest Neighbor Properties Speed-Up of DNA Melting Algorithm with Complete Nearest Neighbor Properties

2004-01-08

arxiv.org/abs/q-bio/0401011v1

Biopolymers, 70, 364-376 (2003)

Biology

Quantitative Biology

Biomolecules

20 pages, 4 figures

Scientific paper

10.1002/bip.10495

We describe a faster and more accurate algorithm for computing the statistical mechanics of DNA denaturation according to the Poland-Scheraga type. Nearest neighbor thermodynamics is included in a complete and general way. The algorithm represents an optimization with respect to algorithmic complexity of the partition function algorithm of Yeramian et al.: We reduce the computation time for a base-pairing probability profile from O(N2) to O(N). This speed-up comes in addition to the speed-up due to a multiexponential approximation of the loop entropy factor as introduced by Fixman and Freire. The speed-up, however, is independent of the multiexponential approximation and reduces time from O(N3) to O(N2) in the exact case. In addition to calculating the standard base-pairing probability profiles, we propose to use the algorithm to calculate various other probabilities (loops, helices, tails) for a more direct view of the melting regions and their positions and sizes.

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