Duplications and pseudo-duplications

Da Jung Cho, Yo-Sub Han, Hwee Kim, Alexandros Palioudakis, Kai Salomaa

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

A duplication is basic phenomenon that occurs through molecular evolution on a biological sequence. A duplication on a string copies any substring of the string. We define k-pseudo-duplication of a string w that consists, roughly speaking, of all strings obtained from w by inserting after a substring u another substring obtained from u by at most k edit operations. We consider three variants of duplication operations, duplication, k-pseudo-duplication and reverse-duplication. First, we give the necessary and sufficient number of states that a nondeterministic finite automaton needs to recognize duplications on a string. Then, we show that regular languages and context-free languages are not closed under the duplication, k-pseudo-duplication and reverse-duplication operations. Furthermore, we show that the class of context-sensitive languages is closed under duplication, pseudo-duplication and reverse-duplication.

Original languageEnglish
Title of host publicationUnconventional Computation and Natural Computation - 14th International Conference, UCNC 2015, Proceedings
EditorsCristian S. Calude, Michael J. Dinneen
PublisherSpringer Verlag
Pages157-168
Number of pages12
ISBN (Print)9783319218182
DOIs
Publication statusPublished - 2015 Jan 1
Event14th International Conference on Unconventional Computation and Natural Computation, UCNC 2015 - Auckland, New Zealand
Duration: 2015 Aug 302015 Sep 3

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9252
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other14th International Conference on Unconventional Computation and Natural Computation, UCNC 2015
CountryNew Zealand
CityAuckland
Period15/8/3015/9/3

Fingerprint

Context sensitive languages
Context free languages
Formal languages
Finite automata
Duplication
Strings
Reverse
Molecular Evolution
Closed
Context-free Languages
Regular Languages

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Cho, D. J., Han, Y-S., Kim, H., Palioudakis, A., & Salomaa, K. (2015). Duplications and pseudo-duplications. In C. S. Calude, & M. J. Dinneen (Eds.), Unconventional Computation and Natural Computation - 14th International Conference, UCNC 2015, Proceedings (pp. 157-168). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9252). Springer Verlag. https://doi.org/10.1007/978-3-319-21819-9_11
Cho, Da Jung ; Han, Yo-Sub ; Kim, Hwee ; Palioudakis, Alexandros ; Salomaa, Kai. / Duplications and pseudo-duplications. Unconventional Computation and Natural Computation - 14th International Conference, UCNC 2015, Proceedings. editor / Cristian S. Calude ; Michael J. Dinneen. Springer Verlag, 2015. pp. 157-168 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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Cho, DJ, Han, Y-S, Kim, H, Palioudakis, A & Salomaa, K 2015, Duplications and pseudo-duplications. in CS Calude & MJ Dinneen (eds), Unconventional Computation and Natural Computation - 14th International Conference, UCNC 2015, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9252, Springer Verlag, pp. 157-168, 14th International Conference on Unconventional Computation and Natural Computation, UCNC 2015, Auckland, New Zealand, 15/8/30. https://doi.org/10.1007/978-3-319-21819-9_11

Duplications and pseudo-duplications. / Cho, Da Jung; Han, Yo-Sub; Kim, Hwee; Palioudakis, Alexandros; Salomaa, Kai.

Unconventional Computation and Natural Computation - 14th International Conference, UCNC 2015, Proceedings. ed. / Cristian S. Calude; Michael J. Dinneen. Springer Verlag, 2015. p. 157-168 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9252).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Cho DJ, Han Y-S, Kim H, Palioudakis A, Salomaa K. Duplications and pseudo-duplications. In Calude CS, Dinneen MJ, editors, Unconventional Computation and Natural Computation - 14th International Conference, UCNC 2015, Proceedings. Springer Verlag. 2015. p. 157-168. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-21819-9_11