Skip to main content
SpringerLink
Log in
Book cover

Algorithmic Bioprocesses pp 313–329Cite as

Finite Splicing: Generative Capacity, New Models and Complexity Aspects

  • Chapter
  • First Online:

  • 1244 Accesses

Part of the book series: Natural Computing Series ((NCS))

Abstract

Splicing systems have been introduced twenty years ago as a basic abstract model of the DNA recombination mechanism. In fact, it was the first of a long series of computational models based on a molecular process. Much research has been done on the generative capacity of these systems, mostly considering enhanced variants of the original definition. However, some important questions about the original finite systems are still unsolved. For example, we do not have any systematic way to go about constructing a splicing system for a given language, and we still lack significant algorithmic results for this model.

In this work, we survey new research directions on finite splicing that could suggest a new approach to the solution of these basic problems and could shed a new light on the splicing formalism. These include an alternative definition of the splicing language, splicing systems as accepting devices, and complexity issues for splicing systems.

Work supported by Research Grants BES-2004-6316 and ES-2006-0146 of the Spanish Ministry of Education and Science.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Birget J-C (1992) Intersection and union of regular languages and state complexity. Inf Process Lett 43:185–190

    Article  MATH  MathSciNet  Google Scholar 

  2. Bonizzoni P, De Felice C, Mauri G, Zizza R (2004) Circular splicing and regularity. Theor Inform Appl 38:189–228

    Article  MATH  MathSciNet  Google Scholar 

  3. Bonizzoni P, De Felice C, Mauri G, Zizza R (2006) Linear splicing and syntactic monoid. Discrete Appl Math 154(3):452–470

    Article  MATH  MathSciNet  Google Scholar 

  4. Bonizzoni P, De Felice C, Mauri G, Zizza R (2005) On the power of circular splicing. Discrete Appl Math 150(1–3):51–66

    Article  MATH  MathSciNet  Google Scholar 

  5. Bonizzoni P, De Felice C, Mauri G, Zizza R (2003) Decision problems on linear and circular splicing. In: Ito M, Toyama M (eds) Proceedings of the DLT 2002. Lecture notes in computer science, vol 2450. Springer, Berlin, pp 78–92

    Google Scholar 

  6. Bonizzoni P, De Felice C, Mauri G, Zizza R (2003) Regular languages generated by reflexive finite linear splicing systems. In: Proceedings of the DLT 2003. Lecture notes in computer science, vol 2710. Springer, Berlin, pp 134–145

    Google Scholar 

  7. Bonizzoni P, De Felice C, Zizza R (2005) The structure of reflexive regular splicing languages via Schützenberger constants. Theor Comput Sci 334(1–3):71–98

    Article  MATH  Google Scholar 

  8. Bonizzoni P, Ferretti C, Mauri G (1998) Splicing systems with marked rules. Rom J Inf Sci Technol 1(4):295–306

    Google Scholar 

  9. Bonizzoni P, Ferretti C, Mauri G, Zizza R (2001) Separating some splicing models. Inf Process Lett 79(6):255–259

    Article  MATH  MathSciNet  Google Scholar 

  10. Bonizzoni P, Mauri G (2006) A decision procedure for reflexive regular splicing languages. Dev Lang Theory 315–326

    Google Scholar 

  11. Calude CS, Păun Gh (2001) Computing with cells and atoms: an introduction to quantum, DNA and membrane computing. Taylor & Francis, London

    MATH  Google Scholar 

  12. Culik K, Harju T (1991) Splicing semigroups of dominoes and DNA. Discrete Appl Math 31:261–277

    Article  MATH  MathSciNet  Google Scholar 

  13. De Luca A, Restivo A (1980) A characterization of strictly locally testable languages and its application to semigroups of free semigroup. Inf Control 44:300–319

    Article  MATH  Google Scholar 

  14. Goode E (1999) Constants and splicing systems. PhD thesis, Binghamton University

    Google Scholar 

  15. Goode E, Pixton D (2007) Recognizing splicing languages: syntactic monoids and simultaneous pumping. Discrete Appl Math 155:988–1006

    Article  MathSciNet  Google Scholar 

  16. Head T (1987) Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviours. Bull Math Biol 49:737–759

    MATH  MathSciNet  Google Scholar 

  17. Head T (1998) Splicing languages generated with one sided context. In: Păun Gh (ed) Computing with bio-molecules. Theory and experiments. Springer, Singapore

    Google Scholar 

  18. Head T, Păun Gh, Pixton D (1996) Language theory and molecular genetics: generative mechanisms suggested by DNA recombination. In: Rozenberg G, Salomaa A (eds) Handbook of formal languages, vol 2. Springer, Berlin, pp 295–360

    Google Scholar 

  19. Kim SM (1997) Computational modeling for genetic splicing systems. SIAM J Comput 26:1284–1309

    Article  MATH  MathSciNet  Google Scholar 

  20. Loos R (2006) An alternative definition of splicing. Theor Comput Sci 358:75–87

    Article  MATH  MathSciNet  Google Scholar 

  21. Loos R, Malcher A, Wotschke D (2008) Descriptional complexity of splicing systems. Int J Found Comput Sci 19(4):813–826

    Article  MATH  MathSciNet  Google Scholar 

  22. Loos R, Martín-Vide C, Mitrana V (2006) Solving SAT and HPP with accepting splicing systems. In: PPSN IX. Lecture notes in computer science, vol 4193. Springer, Berlin, pp 771–777

    Chapter  Google Scholar 

  23. Loos R, Mitrana V (2007) Non-preserving splicing with delay. Int J Comput Math 84(4):427–436

    Article  MATH  MathSciNet  Google Scholar 

  24. Loos R, Ogihara M (2007) Complexity theory for splicing systems. Theor Comput Sci 386:132–150

    Article  MATH  MathSciNet  Google Scholar 

  25. Loos R, Ogihara M (2007) Time and space complexity for splicing systems. Theory Comput Syst (in press)

    Google Scholar 

  26. Păun Gh, Rozenberg G, Salomaa A (1996) Computing by splicing. Theor Comput Sci 168(2):321–336

    Article  MATH  Google Scholar 

  27. Păun G, Rozenberg G, Salomaa A (1998) DNA computing, new computing paradigms. Springer, Berlin

    MATH  Google Scholar 

  28. Perrin D (1990) Finite automata. In: Van Leeuwen J (ed) Handbook of theoretical computer science, vol B. Elsevier, Amsterdam, pp 1–57

    Google Scholar 

  29. Pixton D (1996) Regularity of splicing languages. Discrete Appl Math 69:101–124

    Article  MATH  MathSciNet  Google Scholar 

  30. Schützenberger MP (1975) Sur certaines opérations de fermeture dans le langages rationnels. Symp Math 15:245–253

    Google Scholar 

  31. Stockmeyer L, Meyer AR (1973) Word problems requiring exponential time: preliminary report. In: Fifth annual ACM symposium on theory of computing, pp 1–9

    Google Scholar 

  32. Verlan S, Zizza R (2003) 1-splicing vs. 2-splicing: separating results. In: Proceedings of Words03, Turku, Finland, pp 320–331

    Google Scholar 

  33. Verlan S (2004) Head systems and applications to bio-informatics. PhD thesis, University of Metz

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dipartimento di Informatica Sistemistica e Comunicazione, Università degli Studi di Milano—Bicocca, Viale Sarca 336, 20126, Milano, Italy

    Paola Bonizzoni

  2. EMBL-EBI, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK

    Remco Loos

Authors
  1. Paola Bonizzoni
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Remco Loos
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Paola Bonizzoni .

Editor information

Editors and Affiliations

  1. Dept. Computer Science, University of British Columbia, Main Mall 201-2366, Vancouver, V6T 1Z4, Canada

    Anne Condon

  2. Dept. Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel

    David Harel

  3. Leiden Inst. Advanced Computer Science, Leiden University, Niels Bohrweg 1, Leiden, 2333 CA, Netherlands

    Joost N. Kok

  4. Turku Centre for Computer Science, Lemminkaisenkatu 14 A, Turku, 20520, Finland

    Arto Salomaa

  5. Computer Science, Computation,, California Inst. of Technology, Pasadena, 91125, U.S.A.

    Erik Winfree

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Bonizzoni, P., Loos, R. (2009). Finite Splicing: Generative Capacity, New Models and Complexity Aspects. In: Condon, A., Harel, D., Kok, J., Salomaa, A., Winfree, E. (eds) Algorithmic Bioprocesses. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88869-7_17

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-88869-7_17

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-88868-0

  • Online ISBN: 978-3-540-88869-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation