Abstract
DNA sequence reconstruction is a challenging research problem in the computational biology field. The evolution of the DNA is too complex to be characterized by a few parameters. Therefore, there is a need for a modeling approach for analyzing DNA patterns. In this paper, we proposed a novel framework for DNA pattern analysis. The proposed framework consists of two main stages. The first stage is for analyzing the DNA sequences evolution, whereas the other stage is for the reconstruction process. We utilized cellular automata (CA) rules for analyzing and predicting the DNA sequence. Then, a modified procedure for the reconstruction process is introduced, which is based on the Probabilistic Cellular Automata (PCA) integrated with Particle Swarm Optimization (PSO) algorithm. This integration makes the proposed framework more efficient and achieves optimum transition rules. Our innovated model leans on the hypothesis that mutations are probabilistic events. As a result, their evolution can be simulated as a PCA model. The main objective of this paper is to analyze various DNA sequences to predict the changes that occur in DNA during evolution (mutations). We used a similarity score as a fitness measure to detect symmetry relations, which is appropriate for numerous extremely long sequences. Results are given for the CpG-methylation-deamination processes, which are regions of DNA where a guanine nucleotide follows a cytosine nucleotide in the linear sequence of bases. The DNA evolution is handled as the evolved colored paradigms. Therefore, incorporating probabilistic components help to produce a tool capable of foretelling the likelihood of specific mutations. Besides, it shows their capabilities in dealing with complex relations.