In analyzing gene sequences,various heterogeneous data analysis and a variety of software and algorithms should be integrated.The interactive graphical interface is a prerequisite.A software system named GSAS (gene sequence analysis system) based on Java-based J2EE environment was proposed.The system provides a unified data,algorithm interface and visualization graphical interface,not only integrates a variety of key sequence analysis algorithms and tools,but also achieves the integration of heterogeneous data.The workflow mechanism of GSAS provides a collaborative study solution for analyzing gene sequence.