Abstract
Pattern matching techniques have been useful in solving many problems associated with computer science, including data compression (Chrochemore and Lecroq, 1996), data encryption (RSA Laboratories, 1993), and computer vision (Grimson and Huttenlocher, 1990). In recent years, developments in molecular biology have led to large scale sequencing of genomic DNA. Since this data is being produced in such rapid fashion, tools to analyze DNA segments are desired. The goal here is to discuss various techniques and tools for solving various pattern matching questions in computational biology, including optimal sequence alignment, multiple sequence alignment, and building models to describe sequence families using Hidden Markov Models (HMMs) and regular expressions.
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