Operations and language generating devices suggested by the genome evolution

Abstract

Language-theoretic problems arising from the genome evolution discussed in series of papers (Dassow and Mitrana, Proc. 2nd Pacific Symp. on Biocomputing, World Scientific, Singapore, 1997, pp. 97–108; Bioinformatics, Lecture Notes in Computer Science, vol. 1278, Springer, Berlin, pp. 199–209; Dassow et al., BioSystems 43 (1997) 169–177; Dassow, Jewels are Forever, Springer, Berlin, 1999, pp. 171–181) are presented in a uniform way. The main emphasis is on the operations of inversion, transposition, duplication and deletion suggested by the genome evolution. Basic problems concerning these operations and their iterated versions are settled. A generative device (evolutionary grammar) based on these operations is investigated from different points of view (computational power, decidability problems, descriptional complexity). “Adult languages” (sets of stable strings) of such evolutionary grammars possess a surprising generative power.