The MotifNetwork system is a high performance system for the fast scanning and interpretation of large numbers of proteins into their constituent domains. Once transformed into a domain dataset, several levels of analysis such as domain-domain and protein-protein co-location graphs are constructed. These basic data products form the beginning of a comprehensive environment for work in evolutionary processes with particular support for comparative analysis. MotifNetwork is based on a distributed architecture that has evolved into a reasonably secure system and is currently supporting researchers in drug target identification, ion-channels biophysics, functional orthologs, and socio-genomic processes.

To better support a broader research community, detailed analysis of the performance of several aspects of MotifNetwork are presented. Further, illustrative examples of using the data products in various matrix analyses are provided. Lastly, in conjunction with a recent submission to the BIOCOMP’09 conference, several remaining details on access, usage, and data archiving are summarized rendering fairly complete the technical details, architecture, and software components of the system as well as expected runtimes and results.