Detecting Breakpoints in Whole-Genome Alignments
Author Information
Author(s): Oscar Westesson, Ian Holmes
Primary Institution: University of California Berkeley
Hypothesis
We propose a novel method for detecting sites of molecular recombination in multiple alignments.
Conclusion
Our method accurately detects recombinant regions and breakpoints in genomic sequences, outperforming previous methods.
Supporting Evidence
- We confirm the breakpoint predictions of previous studies and offer novel predictions.
- Our method allows for the analysis of fast-evolving pathogen sequences.
- We demonstrate improved precision and flexibility compared to other programs.
Takeaway
This study introduces a new way to find where genes mix together in viruses and bacteria, helping scientists understand how they evolve.
Methodology
We developed a probabilistic approach using a combined algorithm for estimating tree structure and hidden Markov model parameters to detect changes in phylogenetic tree topology.
Limitations
The method may struggle with high diversity or very short recombinant regions.
Digital Object Identifier (DOI)
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