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Divergence and Shannon information in genomes.
Hong-Da Chen1, Chang-Heng Chang, Li-Ching Hsieh
1Department of Physics, National Central University, Chungli, Taiwan 320, Republic of China.
Physical Review Letters
|May 21, 2005
Summary
Shannon information (SI) in DNA genomes is length-independent and significantly higher than in random sequences, suggesting universal genome growth patterns.
Area of Science:
- Bioinformatics
- Genomics
- Information Theory
Background:
- Shannon information (SI) quantifies sequence complexity.
- Divergence is a special case of SI.
- Genomes vary greatly in length and composition.
Purpose of the Study:
- To compute and compare SI for complete genomes versus random sequences.
- To investigate the relationship between SI, sequence length, and composition.
- To identify universal patterns in genomic SI.
Main Methods:
- Defining SI and divergence based on chemical word probabilities in DNA sequences.
- Calculating SI for a diverse set of complete genomes.
- Comparing genomic SI with SI of matched random sequences.
Main Results:
- Genomic SI is length-independent, unlike random sequences where it's inversely proportional to length.
- Genomic SI is substantially greater than random sequence SI, especially for shorter words and longer sequences.
- Genomic SIs exhibit universal values dependent on word length.
Conclusions:
- Genomic SI's universality suggests a common evolutionary footprint.
- A universal genome growth mode is inferred from these findings.
- SI provides insights into genome evolution and organization.