RNAstructure: software for RNA secondary structure prediction and analysis

<p>Abstract</p> <p>Background</p> <p>To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence.</p> <p>Results</p> <p>RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained.</p> <p>Conclusion</p> <p>The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at <url>http://rna.urmc.rochester.edu/RNAstructure.html</url>.</p

Supercomputing and the Finite Element Approximation of the Navier-Stokes Equations for Incompressible Viscous Fluids

We discuss in this paper the numerical simulation of unsteady incompressible flows modeled by the Navier-Stokes equations, concentrating most particularly on flows at Reynold number of the order of 10^3 to 10^4. The numerical methodology described here is of modular type and well suited to super computers; it is based on time discretization by operator splitting, and space discretization by low order finite element approximations, leading to highly sparse matrices. The Stokes subproblems originating from the splitting are treated by an efficient Stokes solver, particularly efficient for flow at high Reynold numbers; the nonlinear subproblems associated with the advection are solved by a least squares/preconditioned conjugate gradient method. The methodology discussed here is then applied to the simulation of jets in a cavity, using a CRAY X-MP supercomputer. Various visualizations of the numerical results are presented, in order to show the vortex dynamics taking place in the cavity