Comparative Analysis of the Effectiveness of Bioinformatic Tools in miRNA Identification Executive Summary A succinct overview highlighting the main objectives of the study, key findings, and the significance of these results. The primary aim was to validate the effectiveness and accuracy of YASMA in identifying miRNAs, especially in fungi, compared against ShortStack3 and ShortStack4. The findings suggest YASMA's potential to complement existing tools by identifying unique miRNAs not detected by the others. Objective of the Analysis The purpose of this analysis is to validate the effectiveness and accuracy of YASMA in identifying miRNAs, particularly in fungi. This is contrasted against the known efficacy of ShortStack3 and ShortStack4 in miRNA identification in plants, highlighting the potential for YASMA to fill gaps in current bioinformatic tool capabilities. Methodology The study was designed to compare YASMA against ShortStack3 and ShortStack4, with a rationale based on selecting these specific tools for their known performance in miRNA identification. The comparison involved a detailed analysis of miRNA identification numbers, the development and execution of various scripts for data preparation and analysis, and an assessment of the tools' sensitivity and specificity. Results and Discussion Study findings are presented here, highlighting the number of miRNAs identified by each tool and the notable differences among them. This section includes visual graphics with clear legends and detailed explanations, elucidating the indications regarding the tools' sensitivity and specificity. Reflections on the unique identification discrepancies between YASMA and the ShortStack versions are provided, alongside questions arising from the analysis and potential areas for future improvements. Conclusions The main conclusions summarise YASMA's potential to complement ShortStack3 and ShortStack4, offering insights into its unique identification capabilities. Recommendations for further research focus on enhancing tool accuracy and exploring additional genomic contexts where YASMA could provide significant benefits.
