ArticleJournal of theoretical biology2012
Sequence comparison via polar coordinates representation and curve tree.
Article in Journal of theoretical biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- A degeneration-reducing criterion for optimal digital mapping of genetic codes.Computational and structural biotechnology journal · 2019Article
- A Statistical Similarity/Dissimilarity Analysis of Protein Sequences Based on a Novel Group Representative Vector.BioMed research international · 2019Article
- 3D representations of amino acids-applications to protein sequence comparison and classification.Computational and structural biotechnology journal · 2014Article
- Circular Clustering With Polar Coordinate Reconstruction.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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Authors and funding
3 authors.
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Abstract
Sequence comparison has become one of the essential bioinformatics tools in bioinformatics research, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations among the sequences. Existing graphical representation methods have achieved promising results in sequence comparison, but there are some design challenges with the graphical representations and feature-based measures. We reported here a new method for sequence comparison. It considers whole distribution of dual bases and employs polar coordinates method to map a biological sequence into a closed curve. The curve tree was then constructed to numerically characterize the closed curve of biological sequences, and further compared biological sequences by evaluating the distance of the curve tree of the query sequence matching against a corresponding curve tree of the template sequence. The proposed method was tested by phylogenetic analysis, and its performance was further compared with alignment-based methods. The results demonstrate that using polar coordinates representation and curve tree to compare sequences is more efficient.
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