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Natural Computing

, Volume 7, Issue 3, pp 385–401 | Cite as

Solutions to computational problems through gene assembly

  • Artiom Alhazov
  • Ion Petre
  • Vladimir Rogojin
Article

Abstract

Gene assembly in stichotrichous ciliates is an impressive computational process. They have a unique way of storing their genetic information in two fundamentally different forms within their two types of nuclei. Micronuclear genes are broken into blocks (called MDSs), with MDSs shuffled and separated by non-coding material; some of the MDSs may even be inverted. During gene assembly, all MDSs are sorted in the correct order to yield the transcription-able macronuclear gene. Based on the intramolecular model for gene assembly, we prove in this paper that gene assembly may be used in principle to solve computational problems. We prove that any given instance of the Hamiltonian path problem may be encoded in a suitable way in the form of an ‘artificial’ gene so that gene assembly is successful on that gene-like pattern if and only if the given problem has an affirmative answer.

Keywords

DNA computing Ciliates Stichotrichous Gene assembly Hamiltonian path problem Intramolecular model Ciliate-based computing 

Abbreviations

MDS

Macronuclear destined sequence

HPP

Hamiltonian path problem

Notes

Acknowledgements

I. Petre gratefully acknowledges support by Academy of Finland, project 108421. A. Alhazov and V. Rogojin gratefully acknowledge support by Academy of Finland, project 203667, and support by Science and Technology Center in Ukraine, project 4032. V. Rogojin is on leave of absence from Institute of Mathematics and Computer Science of Academy of Sciences of Moldova.

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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Institute of Mathematics and Computer ScienceAcademy of Sciences of MoldovaChisinauMoldova
  2. 2.Academy of FinlandTurkuFinland
  3. 3.Computational Biomodelling LaboratoryÅbo Akademi University, Turku Center for Computer ScienceTurkuFinland
  4. 4.Department of Information TechnologiesÅbo Akademi UniversityTurkuFinland

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