Skip to main content
SpringerLink
Log in

Site-Directed Deletion

  • Conference paper
  • First Online:
Developments in Language Theory (DLT 2018)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 11088))

Included in the following conference series:

Abstract

We introduce a new bio-inspired operation called a site-directed deletion motivated from site-directed mutagenesis performed by enzymatic activity of DNA polymerase: Given two strings x and y, a site-directed deletion partially deletes a substring of x guided by the string y that specifies which part of a substring can be deleted. We study a few decision problems with respect to the new operation and examine the closure properties of the (iterated) site-directed deletion operations. We, then, define a site-directed deletion-closed (and -free) language L and investigate its decidability properties when L is regular or context-free.

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

Access this chapter

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 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight 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

Institutional subscriptions

Notes

  1. 1.

    Site-directed insertion has earlier been considered under the name outfix-guided insertion [2].

References

  1. Aho, A.V., Corasick, M.J.: Efficient string matching: an aid to bibliographic search. Commun. ACM 18(6), 333–340 (1975)

    Article  MathSciNet  Google Scholar 

  2. Cho, D.-J., Han, Y.-S., Ng, T., Salomaa, K.: Outfix-guided insertion. Theor. Comput. Sci. 701, 70–84 (2017)

    Article  MathSciNet  Google Scholar 

  3. Daley, M., McQuillan, I.: Template-guided DNA recombination. Theor. Comput. Sci. 330(2), 237–250 (2005)

    Article  MathSciNet  Google Scholar 

  4. Dassow, J., Mitrana, V., Salomaa, A.: Operations and language generating devices suggested by the genome evolution. Theor. Comput. Sci. 270(1–2), 701–738 (2002)

    Article  MathSciNet  Google Scholar 

  5. Domaratzki, M.: Deletion along trajectories. Theor. Comput. Sci. 320(2–3), 293–313 (2004)

    Article  MathSciNet  Google Scholar 

  6. Enaganti, S.K., Ibarra, O.H., Kari, L., Kopecki, S.: Further remarks on DNA overlap assembly. Inform. Comput. 253(Part 1), 143–154 (2017)

    Article  MathSciNet  Google Scholar 

  7. Enaganti, S.K., Kari, L., Kopecki, S.: A formal language model of DNA polymerase enzymatic activity. Fundam. Inform. 138(1–2), 179–192 (2015)

    MathSciNet  MATH  Google Scholar 

  8. Gasque, P., Dean, Y., McGreal, E., VanBeek, J., Morgan, B.: Complement components of the innate immune system in health and disease in the CNS. Immunopharmacology 49(1), 171–186 (2000)

    Article  Google Scholar 

  9. Han, Y.-S., Ko, S.-K., Ng, T., Salomaa, K.: State complexity of insertion. Int. J. Found. Comput. Sci. 27, 863–878 (2016)

    Article  MathSciNet  Google Scholar 

  10. Han, Y.-S., Ko, S.-K., Salomaa, K.: State complexity of deletion and bipolar deletion. Acta Inform. 53(1), 67–85 (2016)

    Article  MathSciNet  Google Scholar 

  11. Head, T., Pixton, D., Goode, E.: Splicing systems: regularity and below. In: Hagiya, M., Ohuchi, A. (eds.) DNA 2002. LNCS, vol. 2568, pp. 262–268. Springer, Heidelberg (2003). https://doi.org/10.1007/3-540-36440-4_23

    Chapter  Google Scholar 

  12. Ito, M., Kari, L., Thierrin, G.: Insertion and deletion closure of languages. Theor. Comput. Sci. 183(1), 3–19 (1997)

    Article  MathSciNet  Google Scholar 

  13. Kari, L.: Insertion operations: closure properties. Bull. EATCS 51, 181–191 (1993)

    MATH  Google Scholar 

  14. Kari, L.: Deletion operations: closure properties. Int. J. Comput. Math. 52(1–2), 23–42 (1994)

    Article  Google Scholar 

  15. Kari, L., Kopecki, S.: Deciding whether a regular language is generated by a splicing system. In: Stefanovic, D., Turberfield, A. (eds.) DNA 2012. LNCS, vol. 7433, pp. 98–109. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-32208-2_8

    Chapter  Google Scholar 

  16. Kari, L., Thierrin, G.: Contextual insertions/deletions and computability. Inf. Comput. 131(1), 47–61 (1996)

    Article  MathSciNet  Google Scholar 

  17. Knuth, D.E., Morris Jr., J.H., Pratt, V.R.: Fast pattern matching in strings. SIAM J. Comput. 6(2), 323–350 (1977)

    Article  MathSciNet  Google Scholar 

  18. Post, E.L.: A variant of a recursively unsolvable problem. Bull. Am. Math. Soc. 52(4), 264–268 (1946)

    Article  MathSciNet  Google Scholar 

  19. Reikofski, J., Tao, B.Y.: Polymerase chain reaction (PCR) techniques for site-directed mutagenesis. Biotechnol. Adv. 10(4), 535–547 (1992)

    Article  Google Scholar 

Download references

Acknowledgments

We wish to thank the referees for their careful reading of our manuscript and their insightful comments and suggestions that improve the quality of the paper.

Cho was supported by Labex DigiCosme (ANR-11-LABEX-0045-DIGICOSME) operated by ANR as part of the program “Investissement d’Avenir” Idex Paris-Saclay (ANR-11-IDEX-0003-02). Han was supported by the Basic Science Research Program through NRF (2015R1D1A1A01060097) and the International Research & Development Program of NRF (2017K1A3A1A12024971). Kim was supported in part by the NIH grant R01 GM109459. Salomaa was supported by Natural Sciences and Engineering Research Council of Canada Grant OGP0147224.

Author information

Authors and Affiliations

  1. CNRS & LSV, ENS Paris-Saclay, 61, Avenue du Président Wilson, 94235, Cachan Cedex, France

    Da-Jung Cho

  2. LRI, Université Paris-Sud, Bât 650, Rue Noetzlin, 91190, Gif-sur-Yvette, France

    Da-Jung Cho

  3. Department of Computer Science, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, Republic of Korea

    Yo-Sub Han

  4. Department of Mathematics and Statistics, University of South Florida, 12010 USF Cherry Drive, Tampa, FL, 33620, USA

    Hwee Kim

  5. School of Computing, Queen’s University, Kingston, ON, K7L 3N6, Canada

    Kai Salomaa

Authors
  1. Da-Jung Cho
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yo-Sub Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hwee Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kai Salomaa
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yo-Sub Han .

Editor information

Editors and Affiliations

  1. National Archives of Japan, Tokyo, Japan

    Mizuho Hoshi

  2. The University of Electro-Communications, Tokyo, Japan

    Shinnosuke Seki

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Cho, DJ., Han, YS., Kim, H., Salomaa, K. (2018). Site-Directed Deletion. In: Hoshi, M., Seki, S. (eds) Developments in Language Theory. DLT 2018. Lecture Notes in Computer Science(), vol 11088. Springer, Cham. https://doi.org/10.1007/978-3-319-98654-8_18

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-98654-8_18

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-98653-1

  • Online ISBN: 978-3-319-98654-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation