MCALIGN2: A New Method for Aligning Non-Coding DNA Sequences
Author Information
Author(s): Wang Jun, Keightley Peter D, Johnson Toby
Primary Institution: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh
Hypothesis
Can a new method improve the alignment of non-coding DNA sequences compared to existing methods?
Conclusion
MCALIGN2 produces better quality alignments by explicitly using biological knowledge about indel length distribution and nucleotide substitution models.
Supporting Evidence
- MCALIGN2 is up to ten times faster than the previous method MCALIGN.
- MCALIGN2 outperforms heuristic methods like AVID in accuracy for non-coding DNA.
- The method uses a Bayesian statistical framework to compute posterior probabilities for alignments.
- Alignments produced by MCALIGN2 have higher probabilities than those produced by the Monte Carlo method.
Takeaway
MCALIGN2 is a new tool that helps scientists align DNA sequences better by understanding how DNA changes over time.
Methodology
The study developed a new alignment method using a pair-hidden-Markov-Model and tested it against existing methods in simulations.
Limitations
The method may not perform as well with very high divergence times or indel rates.
Digital Object Identifier (DOI)
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