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Validation of predicted anonymous proteins simply using Fisher's exact test
Jean-Michel Claverie1, Sébastien Santini1
1Aix-Marseille University, CNRS, IGS (UMR7256), IMM (FR3479), Luminy, Marseille F-13288, France.
Bioinformatics Advances
|January 26, 2023
Summary
We introduce Fisher's exact test to validate predicted proteins from genome sequencing. This method improves accuracy by analyzing selection pressure, crucial for microbial and viral genomics.
Area of Science:
- Genomics and Bioinformatics
- Molecular Evolution
- Virology
Background:
- Genome sequencing is vital for characterizing new organisms, especially microbes.
- This generates numerous predicted proteins, many lacking validation.
- Current methods for protein validation, like selection pressure analysis, can be error-prone.
Purpose of the Study:
- To introduce a statistically robust method for validating predicted proteins.
- To improve the reliability of protein identification from genomic data.
- To address the challenge of unwarranted protein predictions in microbial genomics.
Main Methods:
- Utilizing Fisher's exact test as a postprocessing step for CODEML software outputs.
- Converting nonsynonymous and synonymous nucleotide change rates into a 2x2 contingency table.
- Applying the test to genome sequences of giant viruses to assess protein existence.
Main Results:
- Demonstrated the application of Fisher's exact test for analyzing selection pressure.
- Showcased how nucleotide change rates can be statistically evaluated.
- Found that strong negative selection pressure does not always confirm protein existence in giant viruses.
Conclusions:
- Fisher's exact test offers a more reliable approach to validating predicted proteins.
- This method enhances the accuracy of genomic data interpretation.
- The study highlights the importance of statistical rigor in bioinformatics analyses.
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