Accelerating calculations of RNA secondary structure partition functions using GPUs.

ABSTRACT:

Background

RNA performs many diverse functions in the cell in addition to its role as a messenger of genetic information. These functions depend on its ability to fold to a unique three-dimensional structure determined by the sequence. The conformation of RNA is in part determined by its secondary structure, or the particular set of contacts between pairs of complementary bases. Prediction of the secondary structure of RNA from its sequence is therefore of great interest, but can be computationally expensive. In this work we accelerate computations of base-pair probababilities using parallel graphics processing units (GPUs).

Results

Calculation of the probabilities of base pairs in RNA secondary structures using nearest-neighbor standard free energy change parameters has bee

SUBMITTER: Stern HA 

PROVIDER: S-EPMC4175106 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature