A generic algorithm for finding restriction sites within DNA sequences |
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| Authors: | Jiang Keyuan; Zheng Jason; Higgins Stanley B |
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| Institution: | Division of Biomedical Engineering and Computing, Vanderbilt University Medical School Nashville, TN 37232–2155
1Hewlett-Packard Co Cupertino, CA 95014, USA |
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| Abstract: | This paper describes a generic algorithm for finding restrictionsites within DNA sequences. The ‘genericity’ ofthe algorithm is made possible through the use of set theory.Basic elements of DNA sequences, i.e. nucleotides (bases), arerepresented in sets, and DNA sequences, whether specific, ambiguousor even protein-coding, are represented as sequences of thosesets. The set intersection operation demonstrates its abilityto perform pattern-matching correctly on various DNA sequences.The performance analysis showed that the degree of complexityof the pattern matching is reduced from exponential to linear.An example is given to show the actual and potential restrictionsites, derived by the generic algorithm, in the DNA sequencetemplate coding for a synthetic calmodulin.
Received on October 2, 1990; accepted on December 18, 1990 |
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