On some operations on strings suggested by gene assembly in ciliates

Authors:
Rudolf Freund;Carlos Martín-Vide;Victor Mitrana
Affiliations:
Institute of Computer Languages, Vienna University of Technology Karlsplatz 13, A-1040 Wien, AUSTRIA;Research Group in Mathematical Linguistics Rovira i Virgili University Pca. Imperial Tàrraco 1, 43005 Tarragona, SPAIN;Faculty of Mathematics, University of Bucharest Str. Academiei 14, 70100, Bucharest, ROMANIA
Venue:
New Generation Computing
Year:
2002

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Abstract

We define three operations on strings and languages suggested by the process of gene assembly in hypotrichous ciliates. This process is considered to be a prime example of DNA computing in vivo. This paper is devoted to some computational aspects of these operations from a formal language point of view. The closure of the classes of regular and context-free languages under these operations is settled. Then, we consider theld macronuclear language of a given language L, which consists of all ld- macronuclear strings obtained from the strings of L by iteratively applying the loop-direct repeat-excision. Finally, we discuss some open problems and further directions of research.