Exact Pattern Matching in Computational Biology: Algorithms and Applications

Pattern matching problem has been studied throughout the history of computer science and is crucial to the computing industry. Over the years, pattern matching algorithms have been extensively applied in various computer applications, for example, in retrieval of information, information security, searching nucleotide or amino acid sequence patterns in biological sequence databases etc. Pattern matching in computational biology arises from the need to know the characteristics of DNA sequences, such as finding the best way to align two sequences or finding any common sub-sequences or determining how well a sequence fits into a given model. Pattern-matching is also used to find mutations in the nucleotide sequences which lead to genetic disorders. Identifying the tricodons helps in predicting the characteristics based on the presence of certain amino acids. In this book, several pattern matching algorithms along with their C language code is covered in detail with applications for addressing nucleotide sequences pattern matching.