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Lecture Notes in Computer Science
Regular expression pattern matching is widely used in computational biology. Searching through a database of sequences for a motif (a simple regular expression), or its variations is an important interactive process which requires fast motif-matching algorithms. In this paper, we explore and evaluate various representations of the database of sequences using suffix trees for two types of query problems for a given regular expression: 1) Find the first match, and 2) Find all matches. Answeringdoi:10.1007/11753728_67 fatcat:ot4lthbmfjhk7nzbtxwaq7sfsm