Structstrings

Structstrings implements the dot bracket annotation for storing base pairing information in structured RNA using Biostrings infrastructure.

Key Features:

• DotBracketString class: Derives the DotBracketString and related classes from the BString class for representing structured RNA.
• Base pair table generation: Produces base pair tables from DotBracketString objects for in-depth analysis.
• Loop index retrieval: Retrieves the loop indices of base pairs from dot bracket annotations.
• Efficient C implementation: Implements information conversion in C for improved computational performance.

Scientific Applications:

• Structured RNA analysis: Enables storage and analysis of RNA secondary structure base pairing information using dot bracket notation.
• RNA base pair analysis: Supports production of base pair tables for detailed investigation of RNA structural features.

Methodology:

Information conversion is implemented in C, inspired largely by the ViennaRNA package.