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ISSCOR: Intragenic, Stochastic Synonymous Codon Occurrence Replacement--a new method for an alignment-free genome
Jan P Radomski1, Piotr P Slonimski
1Interdisciplinary Center for Mathematical and Computational Modeling, Warsaw University, Pawińskiego 5A, Bldg. D, 02106 Warsaw, Poland. janr@icm.edu.pl
Comptes Rendus Biologies
|March 24, 2009
Summary
The sequential order of synonymous codons within genes is not random and is highly constrained, even at long distances. This finding, revealed by the Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR) method, suggests strong selective pressures beyond traditional codon usage.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Synonymous codon frequencies and codon bias are well-studied.
- The sequential arrangement of synonymous codons within genes has not been previously investigated.
Purpose of the Study:
- To develop a computational method to analyze the sequential order of synonymous codons.
- To determine if this sequential order is unique and important for gene function.
Main Methods:
- Development of the Intragenic, Stochastic Synonymous Codon Occurrence Replacement (ISSCOR) method.
- Utilizing Monte Carlo simulations to generate gene sets with permuted codon orders.
- Analysis of the Helicobacter pylori genome using alignment-free computational techniques.
Main Results:
- The succession of synonymous codons, both adjacent and non-adjacent, is significantly non-random.
- Strong constraints on codon order were observed over long nucleotide distances.
- Nucleotide bigram patterns in codon pairs offer a novel method for gene and genome characterization.
Conclusions:
- The sequential order of synonymous codons is under significant selective pressure, independent of classical codon usage.
- The ISSCOR method provides a robust tool for measuring this new dimension of genetic information.
- Findings have implications for comparative genomics and understanding gene function.
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