Two-Step Search for DNA Sequence Design

Satoshi KASHIWAMURA  Atsushi KAMEDA  Masahito YAMAMOTO  Azuma OHUCHI  

IEICE TRANSACTIONS on Fundamentals of Electronics, Communications and Computer Sciences   Vol.E87-A   No.6   pp.1446-1453
Publication Date: 2004/06/01
Online ISSN: 
Print ISSN: 0916-8508
Type of Manuscript: Special Section PAPER (Special Section on Papers Selected from 2003 International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC 2003))
DNA computing,  DNA sequence design problem,  random generator,  two-step search,  

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DNA Sequence Design Problem is a crucial problem in information-based biotechnology such as DNA computing. In this paper, we introduce a powerful design strategy for DNA sequences by refining Random Generator. Random Generator is one of the design strategies and offers great advantages, but it is not a good algorithm for generating a large set of DNA sequences. We propose a Two-Step Search algorithm, then show that TSS can generate a larger set of DNA sequences than Random Generator by computer simulation.