A WEB-BASED GENOMIC INFORMATION SYSTEM FOR EFFICIENTLY MANIPULATING, DISPLAYING AND ACCESSING THE BAC PHYSICAL MAPS OF GENOMES

Department of Soil and Crop Sciences and Crop Biotechnology Center, Texas A&M University, College Station, TX 77843-2123, USA

Genome-wide physical mapping is becoming the centerpiece of modern genomics research. In the past couple of years, we have developed the genome-wide BAC physical maps of the rice (see the poster of Tao et al.) and Arabidopsis thaliana (see the poster of Chang et al.) genomes. To efficiently manipulate the genome physical mapping results and database, and facilitate use of the physical maps in genomics research, we have created a web-based genomic information system (GIS). This system allows users to capture, view, compare, compute, and display graphically the physical mapping research results and database over the web. The system is composed of three parts (layers). The first layer, the user interface (UI), consists of online HTML forms. The second layer, the common gateway interface (CGI), is an intermediate and core layer between the outer layer and the inner layer, and composed of C/C++ programs. The third layer is a static database. The UI is used to carry out user's queries. The CGI is for a set of server applications that deliver and parse the queries, search and manipulate the database, compute and analyze the information, fetch and convert them to UI readable stream, and send back to the users. The result is displayed on user's browser as a graphic contig map, graphic fingerprint patterns, or clone hits. The system is readily portable, accessible and have high performance. It is originally created for and successfully used in the rice and Arabidopsis genome physical mapping projects of our laboratories. It is also well-suited for effectively manipulating, displaying and accessing to the genome physical mapping results and database of any organisms. A web page for use of the system has been posted at http://hbz.tamu.edu/GIS.