A stitch in time: efficient computation of genomic DNA melting bubbles.

ABSTRACT:

Background

It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic.

Results

An efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a maximal bubble length. No approximations, such as windowing, have been introduced to reduce the time complexity. More than just finding the bubbles, the algorithm produces a stitch profile, which is a probabilistic graphical model of bubbles and helical regions. The algorithm applies

SUBMITTER: Tostesen E 

PROVIDER: S-EPMC2553405 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature