Galaxy is an interactive system designed to facilitate large-scale genome analysis by combining existing genome annotation databases with a user-friendly Web portal. It enables users to search remote resources, combine data from independent queries, and visualize results. The core of Galaxy is a flexible history system that stores user queries, performs operations such as intersections, unions, and subtractions, and links to computational tools. Unlike traditional genome browsers, Galaxy does not rely on programming or database skills for more complex analyses. It supports various data manipulation tasks, including query operations, sequence analysis tools, and output displays. Users can combine and compare diverse data sets, such as ENCODE data, to identify specific biological features. Galaxy also allows users to apply molecular evolution algorithms directly to sequences and alignments retrieved through queries. The system is modular, with a central core component orchestrating actions and user histories, and separate UIs and operation toolkits. It uses the BED format for storing query results and supports a variety of data formats. Galaxy's response time is generally quick, and it tracks user identities through cookies. The system is accessible at http://g2.bx.psu.edu.Galaxy is an interactive system designed to facilitate large-scale genome analysis by combining existing genome annotation databases with a user-friendly Web portal. It enables users to search remote resources, combine data from independent queries, and visualize results. The core of Galaxy is a flexible history system that stores user queries, performs operations such as intersections, unions, and subtractions, and links to computational tools. Unlike traditional genome browsers, Galaxy does not rely on programming or database skills for more complex analyses. It supports various data manipulation tasks, including query operations, sequence analysis tools, and output displays. Users can combine and compare diverse data sets, such as ENCODE data, to identify specific biological features. Galaxy also allows users to apply molecular evolution algorithms directly to sequences and alignments retrieved through queries. The system is modular, with a central core component orchestrating actions and user histories, and separate UIs and operation toolkits. It uses the BED format for storing query results and supports a variety of data formats. Galaxy's response time is generally quick, and it tracks user identities through cookies. The system is accessible at http://g2.bx.psu.edu.