Genetic Programming and Evolvable Machines

, Volume 4, Issue 2, pp 153–171

Software Tools for DNA Sequence Design

  • Udo Feldkamp
  • Hilmar Rauhe
  • Wolfgang Banzhaf
Article

DOI: 10.1023/A:1023985029398

Cite this article as:
Feldkamp, U., Rauhe, H. & Banzhaf, W. Genet Program Evolvable Mach (2003) 4: 153. doi:10.1023/A:1023985029398

Abstract

The design of DNA sequences is a key problem for implementing molecular self-assembly with nucleic acid molecules. These molecules must meet several physical, chemical and logical requirements, mainly to avoid mishybridization. Since manual selection of proper sequences is too time-consuming for more than a handful of molecules, the aid of computer programs is advisable. In this paper two software tools for designing DNA sequences are presented, the DNASequenceGenerator and the DNASequenceCompiler. Both employ an approach of sequence dissimilarity based on the uniqueness of overlapping subsequences and a graph based algorithm for sequence generation. Other sequence properties like melting temperature or forbidden subsequences are also regarded, but not secondary structure errors or equilibrium chemistry. Fields of application are DNA computing and DNA-based nanotechnology. In the second part of this paper, sequences generated with the DNASequenceGenerator are compared to those from several publications of other groups, an example application for the DNASequenceCompiler is presented, and the advantages and disadvantages of the presented approach are discussed.

DNA computing DNA nanotechnology molecular self-assembly sequence design specific hybridization 

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Udo Feldkamp
    • 1
  • Hilmar Rauhe
    • 2
  • Wolfgang Banzhaf
    • 1
  1. 1.Chair of Systems AnalysisUniversity of DortmundGermany
  2. 2.Informium AGCologneGermany