## 4 Discussion  
In this section, we discuss the findings and limitations associated with FungiRegEx. Table 1 shows the comparison between FungiRegEx's features and those of the other tools. FungiRegEx highlights this due to its wide coverage, while the other tools cover a maximum of four features. Below, we describe how those features are covered, highlighting the tool's efficiency in data retrieval functionality, which allows for accelerated retrieval of results and optimized use of computational resources because each instance is reused instead of being launched again, compared to other tools that require having the data set archived to perform the search. FungiRegEx does not require downloading the file since it consults the information directly in the database. Users must manually enter characteristics of newly added fungal species to extend them beyond the registered species, potentially limiting their future applicability. \begin{table}
\begin{tabular}{c c c c c c c c c} \hline \hline \multicolumn{1}{c}{ \begin{tabular}{c} **Tool** \\ **Tool** \\ \end{tabular}  } & \multicolumn{1}{c}{\ \begin{tabular}{c} **V** \\ **Tool** \\ \end{tabular}  } & \multicolumn{1}{c}{ \begin{tabular}{c} **X** \\ **Tool** \\ \end{tabular}  } & \multicolumn{FungiRegEx introduces user-friendly features such as real-time data retrieval, customization adaptability since it allows the user to configure the parameters of the instances that can be launched depending on the computational resources available if required, and a Graphical User Interface (see Figure 1), presenting a solution for researchers who do not have the programming knowledge or bash mastery that are necessary for the described tools in the Section 1. Removing FASTA file downloads through the FungiRegEx scrapper module advances real-time data recovery. Still, the dependency on Internet connectivity affects the search speed and varies depending on the quality of the user's connection. Despite this limitation, the tool significantly speeds up result retrieval compared to manual extraction, which could revolutionize large-scale studies. The internet factors, such as speed and availability of computational resources, reveal the need to balance these factors to optimize performance, avoiding issues such as temporary IP blocking when deploying too many scraper instances. Given this last point of implementing scraper instances, it is recommended not to exceed 100 instances in parallel. The efficient use of computational resources underlines the good functioning of FungiRegEx, coupled with the fact that users can configure the parameters for greater control of computational resources. Its adaptability to any computer and customizable parameters improve versatility despite limitations such as single-task support and possible task deletion in simultaneous use scenarios between different users. The GUI simplifies the presentation of results, but readability problems arise in very long proteomes as the table where the results are displayed becomes very large, suggesting room for improvement in the interface. Computer OS independence and deployment flexibility allow users to align runtime modes with their preferences and infrastructure, with a recommendation for local installation due to its single-user nature. Regarding the last six covered features, FungiRegEx does not present any restriction regarding the length limit of the sequence to perform the regular expression search. Also, as mentioned before, this tool does not require the user to have programming knowledge or bash mastery to use it. Another relevant aspect is that this tool does not require a FASTA file; FungiRegEx can perform searches into multiple sequences at the same time. Finally, FungiRegEx allows users to store the results in CSV format if required. The tool's user-defined search parameters improve applicability, although users must specify proteome lengths to perform accurate searches.