RNAlign2D

RNAlign2D aligns multiple RNA molecules by integrating nucleotide sequence and secondary structure information via conversion to pseudo-amino acid sequences to enable rapid structural multiple alignments.

Key Features:

• Pseudo-Amino Acid Substitution Matrix: Converts RNA sequence plus secondary structure into pseudo-amino acid sequences and uses a substitution matrix that integrates structural information for alignment.
• Customizable Scoring Matrix: Provides a configurable scoring matrix tailored to RNA properties to tune alignment scoring.
• Integration with MUSCLE: Acts as a wrapper to apply the protein multiple sequence aligner MUSCLE to pseudo-amino acid representations of RNAs.
• Versatility with Other Aligners: Allows substitution of MUSCLE with other multiple sequence alignment programs to perform alignments on converted sequences.
• Python implementation: Implemented in Python to perform the conversion and alignment orchestration steps.
• Optimized for long sequences and large datasets: Designed to accelerate alignments of long RNA sequences and large datasets by leveraging protein-aligner algorithms on converted sequences.

Scientific Applications:

• Functional Domain Identification: Identifies conserved functional domains in RNAs by aligning sequence and secondary structure information across multiple RNAs.
• RNA Family Classification: Aids classification of RNAs into families based on structural and sequence similarity derived from alignments.
• Discovery of New RNA Functions: Facilitates inference of potential functions for novel RNAs by comparison to structurally aligned known RNAs.

Methodology:

Convert RNA sequences and secondary structure to pseudo-amino acid sequences, apply protein multiple sequence aligners (default MUSCLE) using a customizable scoring/substitution matrix, and orchestrate these steps in Python.