ContigMaker: Software Tool for Contig Map Construction

Akira Suyama[1] (
Masami Hagiya[2] (
Takashi Ito[3]
Asao Fujiyama[4] (
Akira Ohyama[5] (
Toshihisa Takagi[3] (

[1]Institute of Physics, College of Arts and Sciences, The University of Tokyo
3-8-1 Komaba, Meguro-ku, Tokyo 153, Japan
[2]Department of Information Science, Graduate School of Science, The University of Tokyo
7-3-1 Hongo, Bunkyo-ku, Tokyo 113, Japan
[3]Human Genome Center, Institute of Medical Science, The University of Tokyo
4-6-1 Shiroganedai, Minato-ku, Tokyo 108, Japan
[4]Division of Human Genetics, National Institute of Genetics
1111 Yata, Mishima, Shizuoka 411, Japan
[5]Mitsui Knowledge Industry Co. Ltd.
3-7-4 Kojimachi, Chiyoda-ku, Tokyo 102, Japan


ContigMaker is a software tool to aid contig map construction. It is a Motif application running on UNIX workstations with the X Window System. ContigMaker is composed of five major components: map data manager, map analyzer, map viewer, map aid, and project manager. Contig-mapping data obtained by experiments are stored in a database of the map data manager. The stored data are then subjected to analysis by the map analyzer to generate contigs. ContigMaker supports the two strategies for contig construction: the STS (sequence-tagged sites) strategy and the MOF (mapping by oligonucleotide fingerprinting) strategy. The generated contigs are assembled into a contig map according to positions of landmarks falling on the contigs. ContigMaker allows a user to extract landmark information from a public genome database such as the GDB. The contig maps constructed are graphically drawn by the map viewer. The map aid provides miscellaneous small useful tools to finish a contig-mapping task. A repeated task ContigMaker performs can be automated by a macro created by the project manager. The macro will save time and effort for contig map construction.