Gene Phylogenies and Orthologous Groups
João C Setubal1, Peter F Stadler2,3,4,5,6,7
1Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP, 05508-000, Brazil. setubal@iq.usp.br.
Methods in Molecular Biology (Clifton, N.J.)
|December 27, 2017
Summary
This chapter explains ortholog gene set computation, detailing theoretical concepts and practical tools. It guides researchers in identifying orthologous genes using graph-based clustering and available bioinformatics resources.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Ortholog gene set computation is crucial for comparative genomics.
- Understanding orthologs aids in functional inference and evolutionary studies.
Purpose of the Study:
- To provide a comprehensive overview of ortholog gene set computation theory and practice.
- To equip researchers with knowledge of computational methods and tools for identifying orthologous genes.
Main Methods:
- Formal descriptions of theoretical concepts in ortholog identification.
- Explanation of graph-based clustering for ortholog gene set computation.
- Overview of practical considerations and popular software/resources.
Main Results:
- Detailed theoretical framework for ortholog computation.
- Practical guidance for researchers using annotated genomes.
- Summary of current popular programs and resources for ortholog detection.
Conclusions:
- Effective ortholog gene set computation requires understanding both theory and practical tools.
- Researchers can leverage graph-based clustering and available resources for accurate ortholog identification.
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