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Overview and comparison of ortholog databases
Andrey Alexeyenko1, Julia Lindberg1, Asa Pérez-Bercoff1
1Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-106 91, Stockholm, Sweden.
Ortholog databases enable cross-species biological knowledge transfer but vary significantly. This review compares ortholog assignment resources to guide users in selecting the best database for specific research tasks.
Area of Science:
- Genomics
- Bioinformatics
- Comparative Biology
Background:
- Orthologs are crucial for transferring biological information across species.
- Accurate orthology assignment is complex due to diverse methodologies.
- Numerous ortholog databases exist, each with unique characteristics.
Purpose of the Study:
- To compare the content and performance of various ortholog assignment databases.
- To provide guidance on selecting the most appropriate ortholog database for specific research needs.
Main Methods:
- Systematic review of existing ortholog databases.
- Comparative analysis of database content, algorithms, and coverage.
- Evaluation of database suitability for different biological applications.
Main Results:
- Significant heterogeneity exists among ortholog databases.
- Databases differ in their underlying algorithms and data sources.
- No single database is universally superior; suitability depends on the task.
Conclusions:
- Understanding database idiosyncrasies is essential for reliable orthology assignment.
- Choosing the right ortholog database enhances the accuracy of cross-species biological research.
- This review serves as a guide for researchers navigating ortholog resources.
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