NewGenerationComputing,20(2002)279-293 Ohmsha, Ltd. and Springer-Verlag OMPUTING @Ohmsha, Ltd. 2002 On Some Operations on Strings Suggested by Gene Assembly in Ciliates Rudolf FREUND Institute of Computer Languages, Vienna University of Technology Karlsplatz 13, A-1040 Wien, AUSTRIA rudi~logic, at Carlos MARTIN-VIDE Research Group in Mathematical Linguistics Rovira i Virgili University Pfa. Imperial T~rraco 1, 43005 Tarragona, SPAIN cmv@corr eu. urv. es Victor MITRANA Faculty o/Mathematics, University o/Bucharest Str. Academiei 14, 70109, Bucharest, ROMANIA mitrana~funinf, cs. unibuc, ro Received 3 August 2001 Revised manuscript received 4 February 2002 Abstract We define three operations on strings and languages sug- gested by the process of gene assembly in hypotrichous ciliates. This process is considered to be a prime example of DNA computing in vivo. This pa- per 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 the ld-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. Keywords: Molecular Computing, gac-Scheme, Macronuclear String. w Introduction In recent decades, there has been an increasing trend throughout the field of computational biology towards abstract, hierarchical views of biological