MISA-web is a web-based tool for predicting microsatellites, which are short, repeated DNA sequences used as genetic markers. The tool was developed to improve the detection and analysis of microsatellites from nucleotide sequences. The original MISA tool, which was command-line based, had limitations in terms of accessibility and output format. MISA-web addresses these issues by providing an easy-to-use web interface and supporting both proprietary and GFF3 output formats, which are widely used in genomic data analysis. The tool allows users to either paste their nucleotide sequences or input accession numbers to retrieve sequences from the NCBI database. It then processes the sequences to identify microsatellites, which are characterized by short repeated motifs. The tool can detect both perfect and compound microsatellites, which are composed of multiple simple sequence motifs. In a validation study, MISA-web was tested against other microsatellite detection tools on a dataset of barley bacterial artificial chromosomes (BACs). It successfully identified a large number of microsatellites, with most being simple mononucleotide repeats. The tool's performance was comparable to other tools, with execution times similar to those of other programs. MISA-web was found to be particularly effective in detecting microsatellites in protein sequences. The tool is available at http://misaweb.ipk-gatersleben.de/ and provides tutorials, usage notes, and access to the source code. It is supported by the German Federal Ministry of Education and Research (BMBF) under the TRITEX project. The tool is user-friendly and facilitates the integration of microsatellite search results into downstream analysis pipelines.MISA-web is a web-based tool for predicting microsatellites, which are short, repeated DNA sequences used as genetic markers. The tool was developed to improve the detection and analysis of microsatellites from nucleotide sequences. The original MISA tool, which was command-line based, had limitations in terms of accessibility and output format. MISA-web addresses these issues by providing an easy-to-use web interface and supporting both proprietary and GFF3 output formats, which are widely used in genomic data analysis. The tool allows users to either paste their nucleotide sequences or input accession numbers to retrieve sequences from the NCBI database. It then processes the sequences to identify microsatellites, which are characterized by short repeated motifs. The tool can detect both perfect and compound microsatellites, which are composed of multiple simple sequence motifs. In a validation study, MISA-web was tested against other microsatellite detection tools on a dataset of barley bacterial artificial chromosomes (BACs). It successfully identified a large number of microsatellites, with most being simple mononucleotide repeats. The tool's performance was comparable to other tools, with execution times similar to those of other programs. MISA-web was found to be particularly effective in detecting microsatellites in protein sequences. The tool is available at http://misaweb.ipk-gatersleben.de/ and provides tutorials, usage notes, and access to the source code. It is supported by the German Federal Ministry of Education and Research (BMBF) under the TRITEX project. The tool is user-friendly and facilitates the integration of microsatellite search results into downstream analysis pipelines.