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The complexity landscape of viral genomes
Jorge Miguel Silva1, Diogo Pratas1,2,3, Tânia Caetano4
1Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
Gigascience
|August 11, 2022
Summary
This study quantifies viral genome complexity using data compression, revealing DNA viruses exhibit varying redundancy. A new classification method aids in understanding viral genome organization and relationships.
Area of Science:
- Bioinformatics
- Genomics
- Virology
Background:
- Viral genomes are abundant but lack a comprehensive complexity landscape.
- Understanding viral genome organization and characteristics is crucial.
Purpose of the Study:
- To map viral genome complexity and identify redundant/complex viral groups.
- To quantify inverted repeats and analyze local complexity in viral genomes.
- To develop a machine learning-based classification methodology for viral genomes.
Main Methods:
- Utilized data compression algorithms to measure viral genome sequence complexity.
- Applied genomic compressors to extensive viral genome databases.
- Developed complexity profiles for local complexity analysis.
- Combined data compression with GC-content and sequence length for feature-based classification.
Main Results:
- Double-stranded DNA viruses are most redundant; single-stranded DNA viruses are least redundant.
- Double-stranded RNA viruses show lower redundancy than single-stranded RNA viruses.
- Successfully quantified local complexity and performed complexity analysis on human herpesviruses.
- Achieved accurate classification of viral genomes at different taxonomic levels using the developed methodology.
Conclusions:
- The study provides novel methodologies for viral genome characterization and complexity analysis.
- Findings enhance understanding of similarity and singularity patterns among viral groups.
- The developed approach opens new avenues for studying viral genome organization and classification.
Keywords:
algorithmic information theorycladogramsdata compressiongenomicssequence analysisviral classificationvirusesMore Related Videos
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