Exact Search Algorithms for Biological Sequences
Abstract
Pattern matching is a fundamental task in text analyzes, and hence have been heavily exploited in bioinformatics where DNA, RNA, and amino-acid macromolecules are represented as sequences over an alphabet of residue. Examples of analyzes include regulatory motif search and inference, gene identification, repeat finding, association discovery in biomedical literature, etc. We provide an overview of techniques for efficient search of a single or multiple patterns in sequences.
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