Shapiro Group, Computational RNA Structure Group

StructureLab RNA Structure Analysis

StructureLab is a computational system which has been developed to permit the use of a broad array of approaches to the analysis of the structure of RNA. The goal of the development is to provide a large set of tools that can be well integrated with experimental biology to aid in the process of the determination of the underlying structure of RNA sequences.

The approach taken views the structure determination problem as one of dealing with a data base of many computationally generated structures and provides the capability to analyze this data set from different perspectives. Many algorithms are integrated into one system which also utilizes a heterogeneous computing approach permitting the use of several computer architectures to help solve the posed problems. These different computational platforms make it relatively easy to incorporate currently existing programs as well as newly developed algorithms and to match these algorithms to the appropriate hardware.

StructureLab utilizes a network of participating machines defined in reconfigureable tables. A window based interface makes this heterogeneous environment nearly transparent to the user.

The figure (above right) is a general view of some of the available workbench tools in StructureLab (clockwise); the main menu, the taxonomy tree windows, the 2D stem histogram, the Stem Trace control window and a multple solution space plot (data from our massively parallel genetic algorithm, MPGAfold), the structure drawing with base labeling, amino acid labeling, and annotations, a small color scale window, and the large-scale structure drawing.

Specific Capabilities

The following list of specific functional domains is meant to illustrate the major capabilities of the system. It is not an exhaustive list of functions available in STRUCTURELAB.

• Sequence Manipulation
• Folding Algorithms
• Structure Representations
• Structure Alignment
• Taxonomy Operations
• Structure Matching
• RNA Structure Drawing and Manipulation (2D and 3D)
• Two-Dimensional Stem Histogram
• Stem Trace
• Tertiary Interactions Prediction
• Significance/Stability Plots and Energy Plots
• Miscellaneous Functions

For further information and to request a copy, please visit Shapiro Group's StructureLab site