ESEfinder is a web-based tool for identifying exonic splicing enhancers (ESEs), which are regulatory elements that influence pre-mRNA splicing. ESEs are crucial for correct splicing, especially in exons that undergo alternative splicing. Mutations in ESEs can lead to exon skipping, which can cause genetic diseases. ESEfinder uses nucleotide-frequency matrices derived from functional SELEX experiments to predict ESEs responsive to human SR proteins (SF2/ASF, SC35, SRp40, SRp55). The tool allows users to input DNA sequences and predict putative ESEs, as well as assess whether mutations disrupt these elements. ESEfinder has been used to analyze various genes, including BRCA1, BRCA2, FBN1, IGF1, PDHA1, SMN1, SMN2, TNFRSF5, and CFTR. The program uses weight matrices based on frequency values from SELEX experiments, adjusted for background nucleotide composition. It provides both textual and graphical outputs, including scores and color-coded bars representing motif scores. The tool is user-friendly and available for non-commercial use. ESEfinder has been shown to accurately predict ESEs and their disruption in various contexts, including the SMN1 and SMN2 genes. However, the presence of a high-score motif does not necessarily indicate a functional ESE, and other factors such as local sequence context and the presence of silencer elements can influence ESE activity. The tool's matrices were defined in a mammalian system and reflect the sequence specificity of human SR proteins. The development of reliable prediction tools for splicing elements has important implications for understanding gene structure, splicing, and the effects of mutations.ESEfinder is a web-based tool for identifying exonic splicing enhancers (ESEs), which are regulatory elements that influence pre-mRNA splicing. ESEs are crucial for correct splicing, especially in exons that undergo alternative splicing. Mutations in ESEs can lead to exon skipping, which can cause genetic diseases. ESEfinder uses nucleotide-frequency matrices derived from functional SELEX experiments to predict ESEs responsive to human SR proteins (SF2/ASF, SC35, SRp40, SRp55). The tool allows users to input DNA sequences and predict putative ESEs, as well as assess whether mutations disrupt these elements. ESEfinder has been used to analyze various genes, including BRCA1, BRCA2, FBN1, IGF1, PDHA1, SMN1, SMN2, TNFRSF5, and CFTR. The program uses weight matrices based on frequency values from SELEX experiments, adjusted for background nucleotide composition. It provides both textual and graphical outputs, including scores and color-coded bars representing motif scores. The tool is user-friendly and available for non-commercial use. ESEfinder has been shown to accurately predict ESEs and their disruption in various contexts, including the SMN1 and SMN2 genes. However, the presence of a high-score motif does not necessarily indicate a functional ESE, and other factors such as local sequence context and the presence of silencer elements can influence ESE activity. The tool's matrices were defined in a mammalian system and reflect the sequence specificity of human SR proteins. The development of reliable prediction tools for splicing elements has important implications for understanding gene structure, splicing, and the effects of mutations.