Next-generation sequencing has fueled significant advancement in plant breeding tools, such as genome-wide association studies and single-nucleotide polymorphism (SNP) analysis. In this dynamic landscape, plant databases housing SNP markers have evolved into hubs facilitating breeding initiatives and genomic research. PrunusMap, accessible at https://prunusmap.eead.csic.es is an open-source Web application tailored for the Prunus community. Featuring a user-friendly interface, PrunusMap empowers users to seamlessly align and locate markers across multiple genome versions of Prunus species and cultivars, supporting different queries and formats. Beyond locating marker positions, it provides a comprehensive list of annotated nearby genes and proteins. This streamlined process, driven by four intuitive features ‘Find markers’, ‘Align sequences’, ‘Align proteins’, and ‘Locate by position’, significantly reduces workload and boosts efficiency, particularly for users with limited bioinformatics expertise. Moreover, PrunusMap’s versatility is underscored by its commitment to incorporate additional Prunus genome sequences, annotations, and markers upon user request.

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