RB-finder: an improved distance-based sliding window method to detect recombination breakpoints.

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Recombination detection is crucial for understanding pathogen evolution, improving genotyping, and advancing vaccine development.
• Accurate identification of recombination events is essential for reliable phylogenetic analysis.

Purpose of the Study:

• To introduce RB-Finder, a novel, fast, and accurate distance-based window method for detecting recombination in multiple sequence alignments.
• To enhance breakpoint detection accuracy by addressing window size sensitivity.

Main Methods:

• RB-Finder employs a distance-based window approach with an informative distance measure.
• A novel weighting strategy is utilized to minimize sensitivity to window size.
• The method avoids computationally intensive phylogenetic tree construction and comparison.

Main Results:

• RB-Finder demonstrates superior accuracy in recombination breakpoint detection compared to existing phylogeny-based methods.
• The method is significantly more efficient, being hundreds of times faster than the Pruned-PDM method.
• Experimental evaluations on synthetic and biological datasets validate RB-Finder's performance.

Conclusions:

• RB-Finder offers a computationally efficient and accurate solution for recombination detection in sequence data.
• The method has potential applications in genotyping and other related evolutionary analyses.
• This tool can contribute to a better understanding of pathogen evolution and vaccine development.