Algorithms for determining the fate of sites and domain boundaries in computer simulations of recombinant DNA...

Structural and functional features within genomic sequences are best described by their position within the genomic structure. Cleavage sites can be conveniently described by single positions but genomic domains require the position of their two boundaries. The handling of these positions simultaneously to sequence manipulations in computer simulations of recombinant DNA procedures greatly improves the understanding of the resulting recombinant constructs. In addition, the algorithms describing the fate of domain boundaries can be used for the handling of nucleotide sequences in dynamic database environments handled by languages like Prolog which are particularly suitable for artificial intelligence implementations. This communication describes a set of algorithms for the automatic updating of single sites and double domain boundaries in linear and circular models for computer simulation of recombinant DNA procedures.