The authors have developed an integrated software system for analyzing, managing, and distributing data from high-throughput, steady-state expressed sequence tag (EST) projects. The system employs existing public and commercial software where available. Custom software has been developed and integrated as needed. The system was designed to facilitate sequence analysis on remote servers, complex queries of the data, and interactive browsing by nonexpert users. The design of the system was driven by the requirements of providing functionality with a short development time. The analysis procedures and database structures used in this system are not specific to a laboratory and could be used by an EST project or other project directed toward sequencing and mapping short sequence tags, including genomic sequence-tagged sites or tags generated by random amplification of polymorphic DNA mapping.