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Numerical Characterization of DNA Sequences for Alignment-free Sequence Comparison - A Review
Natarajan Ramanathan1, Jayalakshmi Ramamurthy2, Ganapathy Natarajan3
1Department of Chemistry, Sri Sarada Niketan College for Women, Karur-639005, Tamil Nadu,India.
Combinatorial Chemistry & High Throughput Screening
|August 12, 2021
Summary
Alignment-free DNA sequence comparison using numerical characterization offers superior phylogenetic analysis. This approach, utilizing DNA invariants, enhances evolutionary relationship studies and aids in designing peptide-based vaccines for infectious diseases.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Biological macromolecules like DNA, RNA, and protein sequences encode evolutionary history.
- Multiple Sequence Alignment (MSA) is traditionally used for studying evolutionary relationships but has limitations.
- Alignment-free methods using numerical characterization of DNA sequences offer an alternative approach.
Purpose of the Study:
- To review alignment-free DNA sequence comparison methods based on numerical characterization.
- To present the evolution of numerical characterization from graphical representations for phylogenetic analysis.
- To discuss the application of DNA invariants in constructing phylogenetic trees.
Main Methods:
- Graphical representation of DNA sequences (e.g., chaos game representation, 2D/3D methods).
- Numerical characterization of DNA sequences to compute DNA invariants.
- Extension of chemometric molecular descriptors to calculate new DNA invariants.
- Alignment-free sequence comparison in N-dimensional space.
Main Results:
- Phylogenetic trees constructed using DNA invariants were superior to those from alignment-based tools (e.g., PHLYIP, ClustalW).
- Graphical representation methods combined with numerical characterization can identify conserved regions in viral sequences.
- This approach aids in designing peptide-based vaccines for infectious diseases.
Conclusions:
- Alignment-free DNA sequence comparison using numerical characterization provides robust phylogenetic insights.
- The methods are effective for studying evolutionary relationships and can be applied to viral sequences.
- This approach has potential applications in vaccine design for infectious diseases.
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