PROMPT is a system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatic data retrieval and integration, many analysis and comparison algorithms, and a full-featured GUI application. Exhaustive statistical tests are conducted automatically in appropriate cases, but can be performed manually. All analysis results can be viewed or visualized and exported in various formats. All methods can be used in your own Java code or with beanshell scripting in your own scripts, a pipeline, or grid systems. (Source: