GTfold: enabling parallel RNA secondary structure prediction on multi-core desktops.

ABSTRACT:

Background

Accurate and efficient RNA secondary structure prediction remains an important open problem in computational molecular biology. Historically, advances in computing technology have enabled faster and more accurate RNA secondary structure predictions. Previous parallelized prediction programs achieved significant improvements in runtime, but their implementations were not portable from niche high-performance computers or easily accessible to most RNA researchers. With the increasing prevalence of multi-core desktop machines, a new parallel prediction program is needed to take full advantage of today's computing technology.

Findings

We present here the first implementation of RNA secondary structure prediction by thermodynamic optimization for modern multi-core compu

SUBMITTER: Swenson MS 

PROVIDER: S-EPMC3748833 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature