Site-Directed Deletion

Da Jung Cho; Yo Sub Han; Hwee Kim; Kai Salomaa

doi:10.1007/978-3-319-98654-8_18

Site-Directed Deletion

Da Jung Cho, Yo Sub Han, Hwee Kim, Kai Salomaa

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Citation (Scopus)

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.

Original language	English
Title of host publication	Developments in Language Theory - 22nd International Conference, DLT 2018, Proceedings
Editors	Mizuho Hoshi, Shinnosuke Seki
Publisher	Springer Verlag
Pages	219-230
Number of pages	12
ISBN (Print)	9783319986531
DOIs	https://doi.org/10.1007/978-3-319-98654-8_18
Publication status	Published - 2018
Event	22nd International Conference on Developments in Language Theory, DLT 2018 - Tokyo, Japan Duration: 2018 Sep 10 → 2018 Sep 14

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	11088 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	22nd International Conference on Developments in Language Theory, DLT 2018
Country/Territory	Japan
City	Tokyo
Period	18/9/10 → 18/9/14

Bibliographical note

Funding Information:
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.

Publisher Copyright:
© 2018, Springer Nature Switzerland AG.

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
Computer Science(all)

Access to Document

10.1007/978-3-319-98654-8_18

Cite this

Cho, D. J., Han, Y. S., Kim, H., & Salomaa, K. (2018). Site-Directed Deletion. In M. Hoshi, & S. Seki (Eds.), Developments in Language Theory - 22nd International Conference, DLT 2018, Proceedings (pp. 219-230). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11088 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-98654-8_18

Cho, Da Jung ; Han, Yo Sub ; Kim, Hwee ; Salomaa, Kai. / Site-Directed Deletion. Developments in Language Theory - 22nd International Conference, DLT 2018, Proceedings. editor / Mizuho Hoshi ; Shinnosuke Seki. Springer Verlag, 2018. pp. 219-230 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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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.",

author = "Cho, {Da Jung} and Han, {Yo Sub} and Hwee Kim and Kai Salomaa",

note = "Funding Information: Cho was supported by Labex DigiCosme (ANR-11-LABEX-0045-DIGICOSME) operated by ANR as part of the program “Investissement d{\textquoteright}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. Publisher Copyright: {\textcopyright} 2018, Springer Nature Switzerland AG.; 22nd International Conference on Developments in Language Theory, DLT 2018 ; Conference date: 10-09-2018 Through 14-09-2018",

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Cho, DJ, Han, YS, Kim, H & Salomaa, K 2018, Site-Directed Deletion. in M Hoshi & S Seki (eds), Developments in Language Theory - 22nd International Conference, DLT 2018, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 11088 LNCS, Springer Verlag, pp. 219-230, 22nd International Conference on Developments in Language Theory, DLT 2018, Tokyo, Japan, 18/9/10. https://doi.org/10.1007/978-3-319-98654-8_18

Site-Directed Deletion. / Cho, Da Jung; Han, Yo Sub; Kim, Hwee; Salomaa, Kai.

Developments in Language Theory - 22nd International Conference, DLT 2018, Proceedings. ed. / Mizuho Hoshi; Shinnosuke Seki. Springer Verlag, 2018. p. 219-230 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 11088 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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N1 - Funding Information: 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. Publisher Copyright: © 2018, Springer Nature Switzerland AG.

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N2 - 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.

AB - 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.

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Cho DJ, Han YS, Kim H, Salomaa K. Site-Directed Deletion. In Hoshi M, Seki S, editors, Developments in Language Theory - 22nd International Conference, DLT 2018, Proceedings. Springer Verlag. 2018. p. 219-230. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-98654-8_18

Site-Directed Deletion

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