FungiRegEx: A Tool for Pattern Identification in Fungal Proteomic Sequences Using Regular Expressions

Abstract

In the context of proteomic-scale research, it is imperative to automatically analyze numerous species and subspecies to discern distinctive characteristics present in multiple species of the fungi kingdom that contain sequences of interest that could fulfill a specific biological function. To achieve this, complex sequences must be recognized within an organism’s entire set of proteomes. Our study presents FungiRegEx, a piece of software that facilitates the identification of regular expressions of proteomes of fungal organisms and uses real-time data retrieval of the different species from the JGI Mycocosm database without the need to download any file. Integrating a graphical user interface that makes it easy to use, the tool offers regular expression searches on 2402 fungal species from the JGI Mycocosm portal. The tool was validated with the AXSXG sequence and the RXRL effector, demonstrating the effectiveness of FungiRegEx in identifying user-defined patterns in the recovered sequences. This tool allows customization and filtering, and it can save results if required, combining speed, adaptability, and ease of use. It provides an experience without a console and programming, displaying the results in a GUI and making them easier to read. Its architecture guarantees optimized use of resources, time consumption, and implementation flexibility, allowing the customization of specific software parameters for resource management. The tool’s potential for future research and exploration is emphasized, providing a nuanced perspective on its practical use within the fungal genomics community. The tools are available at the addresses mentioned in the text.

Keywords

• proteome analysis
• FungiRegEx
• regular expressions finding
• bioinformatics