Duplications and pseudo-duplications

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

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

A duplication is one of the basic phenomena that occur in molecular evolution on a biological sequence. A duplication on a string is a process of copying a substring of the string—Given w = x1x2x3, a duplication of w is x1x2x2x3. We define k-pseudo-duplication of a string w to be a set of all strings obtained from w by inserting after a substring u of w another substring uʹ such that the edit distance between u and uʹ is at most k. We consider duplication, k-pseudo-duplication and reverse duplication as operations on formal languages. First, we demonstrate that regular languages and context-free languages are not closed under the duplication, k-pseudo-duplication and reverse-duplication operations. Second, we show that context-sensitive languages are closed under duplication, pseudo-duplication and reverse-duplication. Last, we present the necessary and sufficient number of states that a nondeterministic finite automaton needs to recognize all duplications of a string with respect to the string length.

Original languageEnglish
Pages (from-to)145-167
Number of pages23
JournalInternational Journal of Unconventional Computing
Volume12
Issue number2-3
Publication statusPublished - 2016 Jan 1

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Formal languages
Context sensitive languages
Context free languages
Copying
Finite automata

All Science Journal Classification (ASJC) codes

  • Computer Science(all)

Cite this

Cho, D. J., Han, Y. S., Kim, H., Palioudakis, A., & Salomaa, K. (2016). Duplications and pseudo-duplications. International Journal of Unconventional Computing, 12(2-3), 145-167.
Cho, Da Jung ; Han, Yo Sub ; Kim, Hwee ; Palioudakis, Alexandros ; Salomaa, Kai. / Duplications and pseudo-duplications. In: International Journal of Unconventional Computing. 2016 ; Vol. 12, No. 2-3. pp. 145-167.
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Cho, DJ, Han, YS, Kim, H, Palioudakis, A & Salomaa, K 2016, 'Duplications and pseudo-duplications', International Journal of Unconventional Computing, vol. 12, no. 2-3, pp. 145-167.

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

In: International Journal of Unconventional Computing, Vol. 12, No. 2-3, 01.01.2016, p. 145-167.

Research output: Contribution to journalArticle

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Cho DJ, Han YS, Kim H, Palioudakis A, Salomaa K. Duplications and pseudo-duplications. International Journal of Unconventional Computing. 2016 Jan 1;12(2-3):145-167.