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GOThresher: a program to remove annotation biases from protein function annotation datasets.

Parnal Joshi^1,2, Sagnik Banerjee^1,3, Xiao Hu²

¹Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA.

Bioinformatics (Oxford, England)

|January 23, 2023

Summary

This summary is machine-generated.

GOThresher is a new Python tool that identifies and removes biases in gene function annotation databases. This ensures more accurate protein function prediction for machine learning and a better understanding of the annotation landscape.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

High-throughput sequencing generates vast genomic data, but gene product functions remain largely unknown.
Current experimental methods cannot keep pace with the data influx, leading to biased annotations.
Biases in Gene Ontology (GO) terms affect protein function understanding and machine learning model training.

Purpose of the Study:

To address the challenge of biased protein function annotations.
To introduce a computational tool for identifying and removing biases in annotation databases.

Main Methods:

Development of GOThresher, a Python-based software tool.
Implementation of algorithms to detect and correct biases in Gene Ontology annotations.

Main Results:

GOThresher effectively identifies and removes biases from protein function annotation databases.
The tool facilitates the creation of more accurate and representative annotation datasets.

Conclusions:

Removing biases is crucial for accurate protein function prediction and understanding.
GOThresher provides a valuable resource for the bioinformatics community to improve annotation quality.