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Orthoweb: a software package for evolutionary analysis of gene networks
R A Ivanov1, A M Mukhin2, F V Kazantsev2
1Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
Vavilovskii Zhurnal Genetiki I Selektsii
|February 13, 2025
Summary
Orthoweb is a new software tool for calculating evolutionary indices like phylostratigraphic age index (PAI) and divergence indices (Ka/Ks). It aids in understanding gene evolution, transcriptome dynamics, and functional genomics through integrated network analysis and pre-computed data.
Area of Science:
- Evolutionary Biology
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Understanding gene evolutionary trajectories and their functional implications is crucial for deciphering organismal development and adaptation.
- Existing tools may lack integrated approaches for analyzing various evolutionary indices across genes and networks.
- Assessing the evolutionary age and divergence of genes and transcriptomes requires robust computational methods.
Purpose of the Study:
- To introduce Orthoweb, a comprehensive software package for calculating diverse evolutionary indices.
- To enable integrated analysis of phylostratigraphic indices, divergence indices (Ka/Ks), and transcriptome dynamics.
- To facilitate functional enrichment and SNP enrichment analyses linked to evolutionary origins.
Main Methods:
- Development of Orthoweb software for calculating phylostratigraphic age index (PAI), transcriptome age index (TAI), and transcriptome divergence index (TDI).
- Integration of gene network analysis with evolutionary index calculations.
- Inclusion of Gene Ontology (GO) term exploration and SNP enrichment analysis tools.
- Provision of a pre-calculated index database accessible via API.
Main Results:
- Orthoweb provides a unified platform for calculating and visualizing multiple evolutionary indices for individual genes and gene networks.
- The software enables the assessment of evolutionary age and divergence across taxa.
- Advanced visualization tools facilitate the interpretation of complex evolutionary relationships within gene networks.
- Pre-computed data and API access streamline computational workflows.
Conclusions:
- Orthoweb offers a powerful and integrated solution for evolutionary genomics research.
- The software enhances the understanding of gene and transcriptome evolution, functional genomics, and adaptation.
- Orthoweb's features support efficient exploration of evolutionary patterns and genetic variation.
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