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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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PCV: An Alignment Free Method for Finding Homologous Nucleotide Sequences and its Application in Phylogenetic Study
Rajnish Kumar1, Bharat Kumar Mishra1, Tapobrata Lahiri2
1Department of Applied Science, Indian Institute of Information Technology - Allahabad, Allahabad, UP, 211012, India.
Interdisciplinary Sciences, Computational Life Sciences
|January 31, 2016
Summary
This study introduces a novel numerical gene representation called Periodicity Count Value (PCV). PCV reduces computational cost for sequence comparison and aids in molecular phylogeny, offering a more efficient alternative to traditional alignment methods.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Sequence alignment is crucial for retrieving homologous nucleotide sequences.
- Existing methods rely on local alignment and scoring matrices, facing limitations in computational complexity and accuracy.
- A need exists for more efficient and accurate methods for gene sequence representation and comparison.
Purpose of the Study:
- To introduce a novel numerical representation for gene sequences.
- To reduce computational cost in calculating distances between gene pairs.
- To assess the utility of this new representation in molecular phylogeny.
Main Methods:
- Development of a 36-dimensional Periodicity Count Value (PCV) based on physicochemical properties and positional distribution of nucleotides.
- Adaptation from the stochastic model proposed by Kolekar et al.
- Application of PCV in molecular phylogeny constructs for comparison with existing sequence alignment methods.
Main Results:
- PCV provides a numerical representation of nucleotide sequences.
- PCV significantly reduces computational cost in calculating distances between gene pairs.
- PCV-based methods demonstrate consistency with existing methods and validity in molecular phylogeny.
Conclusions:
- The Periodicity Count Value (PCV) offers an efficient numerical representation for gene sequences.
- PCV enhances computational efficiency in sequence comparison and distance calculation.
- PCV is a viable and effective tool for applications like molecular phylogeny.
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