CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures

Area of Science:

• Bioinformatics
• Computational Biology
• Molecular Evolution

Background:

• Compensatory base changes (CBCs) are crucial for understanding RNA secondary structure evolution and species differentiation.
• Existing bioinformatics tools may not efficiently integrate the analysis of CBCs within multiple sequence alignments for phylogenetic reconstruction.

Purpose of the Study:

• To introduce CBCAnalyzer, a novel software toolbox for detecting and analyzing CBCs.
• To provide a user-friendly interface for processing RNA sequence data and reconstructing phylograms.

Main Methods:

• The CBCAnalyzer toolbox comprises three modules: CTTransform for file format conversion, CBCDetect for CBC counting in alignments, and CBCTree for phylogenetic tree reconstruction using the BIONJ algorithm.
• Input formats include various ct-files, processed into a bracket-dot-bracket format compatible with other RNA analysis tools.
• CBCDetect analyzes all-against-all sequence alignments generated by tools like MARNA to identify CBCs, crucial for detecting sexually incompatible species.

Main Results:

• CBCAnalyzer successfully integrates RNA sequence manipulation, CBC detection, and phylogenetic analysis.
• The toolbox provides a distance matrix from CBC counts, enabling the reconstruction of accurate phylograms.
• Application examples demonstrate the utility of CBCAnalyzer in evolutionary and genetic studies.

Conclusions:

• CBCAnalyzer offers a comprehensive and accessible solution for analyzing compensatory base changes in RNA sequences.
• The software facilitates the identification of species-specific genetic markers and aids in evolutionary relationship studies.
• The freely available toolbox with a graphical user interface promotes wider adoption in bioinformatics research.