RNAmountAlign

RNAmountAlign aligns RNA sequences together with secondary-structure information to detect structural homology and assess statistical significance.

Key Features:

• Algorithm Efficiency: O(n³) time and O(n²) space complexity using an incremental mountain height representation to encode structural information.
• Alignment Types: Supports pairwise local, global, and semiglobal alignments and progressive multiple sequence alignments.
• Statistical Validation: Provides Karlin-Altschul p-values for local alignments that can be converted to expect values (E-values).
• Parameter Fitting: Includes parameter fitting options for both local and global alignments.
• Scanning Capability: RNAmountAlignScan scans target genome sequences to identify regions of high sequence and structural similarity and reports improved speed and accuracy relative to RSEARCH and FOLDALIGN.
• Benchmarking Performance: Benchmarked against LocARNA, LARA, FOLDALIGN, DYNALIGN, STRAL, MXSCARNA, and MUSCLE, showing comparable accuracy with faster runtime across alignment types.

Scientific Applications:

• Identification of functional RNA structures: Detects functionally relevant RNA structures by integrating sequence and base-pairing information.
• Comparative structural RNA analysis: Compares RNA molecules across species or conditions to investigate evolutionary relationships.
• Genome annotation of conserved RNA elements: Assists annotation of newly sequenced genomes by identifying structurally conserved RNA elements.

Methodology:

Implements a weighted combination of sequence and structural similarity and uses an incremental mountain height representation (O(n³) time, O(n²) space) to encode structure; provides quadratic-time implementations for pairwise local, global, and semiglobal alignments; applies Karlin-Altschul statistics for local alignment p-values/E-values; and includes RNAmountAlignScan for genome-scale scanning.