Further Improvements on SMART: Sequence Motif Analysis and Retrieval Tool

A. Ogiwara[1] (ogi@ims.u-tokyo.ac.jp)
I. Uchiyama[2] (uchiyama@kuicr.kyoto-u.ac.jp)
T. Takagi[1] (takagi@ims.u-tokyo.ac.jp)
M. Kanehisa[2] (kanehisa@kuicr.kyoto-u.ac.jp)

Human Genome Center,
Institute of Medical Science, The University of Tokyo
4-6-1 Shirokanedai, Minato-ku, Tokyo 108, Japan
[2] Institute for Chemical Research, Kyoto University
Gokasho, Uji, Kyoto 611, Japan


We present further improvements on the computer system SMART (sequence motif analysis and retrieval tool) that assists biological interpretation of sequence data by searching sequence motifs in a query sequence and annotating functional features associated with the motifs found. The new version of the system fully utilizes the network communication based on a client-server model so that users run only the client program on their workstations without any database resources locally. In the previous version, SMART could treat either PROSITE or MotifDic as a motif dictionary, but in the new release, a new motif dictionary characterizing structural groups derived from PDB is also available. SMART runs on Sun workstations using the XView graphical user interface.