Utilization of Cellular Automata in the DNA Signal Search Problem

Abstract

Time-varying cellular automata (TV CA) are a form of cellular automata (CA) where the transition functions vary over time or are time de- pendent. The DNA signal search problem (DSSP) is a well-known problem in bio-informatics. Es- sentially it is the problem of searching for patterns in biological sequences. Two classical approaches utilize computation theory to exploit the power of deterministic ßnite automata (DFA). A third approach uses a ßltering technique. CA is novel in DSSP. We view a CA as an ag- gregate of NFAs or cells where the NFA transitions are modißed to account for neighboring cell states. There is a large body of literature on CA and large body of literature on NFA in DSSP. In this paper we extend the classical approach and explain the us- age of a TV CA in DSSP.