This paper focuses on Watson-Crick languages inspired by DNA computing, their models, and algorithms for deciding the language membership. It analyzes a recently introduced algorithm called WK-CYK introduces state space search that is based regular Breadth-first but uses number of optimizations heuristics to be efficient in practical use able analyze longer inputs. The key parts are pruning (de...

In this work, we analyze the computational power of Watson-Crick finite automata (WKFA) if some restrictions over transition function in model are imposed. We consider that imposed refer to maximum length difference between two input strands which is called delay. prove language class accepted by WKFA with such a proper subclass languages arbitrary general. addition, initiate study classes char...

We consider stateless counter machines which mix the features of one-head counter machines and a special type of two-head Watson-Crick automata (WK-automata). Our biologically motivated machines have heads that read the input starting from the two extremes. The reading process is finished when there are no more symbols between the heads. Depending on whether the heads are required to advance at...

The existence and identity of non-Watson-Crick base pairs (bps) within RNA bulges, internal loops, and hairpin loops cannot reliably be predicted by existing algorithms. We have developed the Isfold (Isosteric Folding) program as a tool to examine patterns of nucleotide substitutions from sequence alignments or mutation experiments and identify plausible bp interactions. We infer these interact...