FungiRegEx: A tool for patterns identification in Fungal Proteomic sequences using regular expressions

Abstract

Abstract In the context of genome-scale research, it is imperative to automatically analyze numerous species and sub-species to discern distinctive features present in multiple proteomes that contain specific sequences of interest since they provide specific properties. Complex sequences must be recognized within an organism’s complete set of proteomes to accomplish this. This study introduces FungiRegEx, a user-friendly software for automatic genome-scale proteome analysis of fungi organisms, addressing the limitations of existing tools. FungiRegEx utilizes real-time data retrieval of the different species from the JGI Mycocosm database without downloading any files. With a user-friendly GUI, the tool offers efficient regular expression searches across 2,402 fungal species from the JGI Mycocosm portal. Validation with the sequence AXSXG or effector RXRL demonstrates FungiRegEx’s effectiveness in identifying user-defined patterns in the retrieved sequences. FungiRegEx accelerates result retrieval compared to manual processes, providing a console-free and programming-free experience; this tool allows customization, result filtering, and the possibility of saving the results for future research. FungiRegEx offers a promising solution for researchers exploring specific sequences in the fungal proteomes. It combines speed, adaptability, and ease of use, displaying the results in a GUI and making it easy to read. Its architecture ensures optimized resource usage and deployment flexibility, allowing the customization of specific software parameters. The tool’s potential for future research and exploration is emphasized, providing a nuanced perspective on its practical use within the fungal genomics community.