Developing Support System for Sequence Design in DNA Computing

Sequence design is the important factor which governs the reaction of DNA. In related researches, the method to minimize (or maxmize) the evaluation function based on knowledge of sequence design has been used. In this paper, we develop support system for sequence design in DNA computing, which minimizes the evaluation function calculated as the linear sum of the plural evaluation terms. Our system not only searches for good sequences but also presents contribution ratio of each evaluation term to the evaluation function and can reduce the number of combination of evaluation terms by reduction of the evaluation function. It helps us to find a good criteria for sequence design in DNA computing.

Authors and Affiliations

1. Division of Systems and Information Eng., Graduate School of Eng., Hokkaido University, Japan

   Fumiaki Tanaka, Masashi Nakatsugawa, Masahito Yamamoto & Azuma Ohuchi1

2. Division of Molecular Chemistry Eng., Graduate School of Eng., Hokkaido University, Nishi 8, Kita 13, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan

   Toshikazu Shiba

Editors and Affiliations

1. Department of Mathematics, University of South Florida, 4202 E. Fowler A. PHY 114, Tampa, FL, 33620, USA

   Nataša Jonoska

2. Department of Chemistry, New York University, New York, NY, 10003, USA

   Nadrian C. Seeman

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