SStructView

SStructView visualizes RNA secondary structures by providing pre-computed two-dimensional layouts and integration with computational backends for structural analysis.

Key Features:

• Domain Graphics: Represents RNA secondary structures using standard two-dimensional "domain graphics" layouts.
• Pre-computed Layouts and Selection: Provides pre-computed RNA layouts and supports selection of bases, helices, and subsequences to supply information to associated application programs.
• Computational Backend Integration: Integrates with BLAST, Medline, and the RNA MFOLD search/compute engines.
• Decoupled Architecture: Decouples graphical representations from computation engines to enable reuse of graphical components across computational backends.

Scientific Applications:

• Sequence Analysis: Facilitates use of BLAST and related services for sequence-based queries tied to structural contexts.
• Database Searching: Supports linking structural representations to Medline for literature-anchored investigations.
• RNA Folding Prediction: Supports integration with RNA MFOLD for predictive modeling of RNA secondary structure folding patterns.
• Structure–Function Studies: Enables analysis that connects secondary-structure features to investigations of RNA function and structure.

Methodology:

Uses domain-specific "domain graphics" as reusable 2D layouts, decouples graphical representations from computation engines, and links those representations to BLAST, Medline, and the RNA MFOLD search/compute engines.