A Deductive Method for Construction and Visualization of Contigs in the STS Strategy

Masami Hagiya (hagiya@is.s.u-tokyo.ac.jp)

Department of Information Science
Graduate School of Science, University of Tokyo
7-3-1 Hongo, Bunkyo-ku, Tokyo 113 Japan


The problem of constructing contigs by the STS strategy is a simple combinatorial problem if the given hit information is correct and complete. However, hit information is often incorrect or incomplete due to failure or inability of experiments. Moreover, in addition to hit information, various sources of information are also available, such as known landmarks, other clone libraries, etc. In order to cope with incompleteness, incorrectness and additional information, we developed a deductive method for constructing contigs. Contigs are constructed by deducing an equivalence relation of clone directions and a partial order among STS markers on each equivalence class of directions. In the paper, a practical algorithm based on the method is presented and its completeness is proved. The method is also axiomatized by a set of inference rules for deducing the equivalence relation and the partial orders. We finally discuss the problem of visualizing contigs based on the information deduced by our method.