Abstract: A genomic database system that makes use of autonomous agents for providing access to the database. The autonomous agents, which are preferably implemented in a multitasking environment, each seek target data to be processed and then call a program to process the target data. The results of the program are then placed in the database. The autonomous agent model permits the sequence data and processing programs to be changed without the need to be concerned with data synchronization or heterogeneity. The agents may be implemented as object oriented programs that permit the extraction of generic software code in an agent code base. The agents may implement annotation functions, analysis algorithms, or may control the assembly of gene sequences.