Super-pattern matching

Allen, F. E. Control Flow Analysis.SIGPLAN Notices,5 (1970), 1–19.

Arbarbanel, R. M., P. R. Wieneke, E. Mansfield, D. A. Jaffe, and D. L. Brutlag. Rapid Searches for Complex Patterns in Biological Molecules.Nucleic Acids Res.,12(1) (1984), 263–280.

Brzozowski, J. A. Derivatives of Regular Expressions.J. Assoc. Comput. Mach.,11 (1964), 481–494.

Barley, J. An Efficient Context-Free Parsing Algorithm.Comm. ACM,13(2) (1970), 94–102.

Fields, C. A., and C. A. Soderlund. gm: A Practical Tool for Automating DNA Sequence Analysis.CABIOS,6 (1990), 263–270.

Fujisaki, T., T. E. Chefalas, J. Kim, C. C. Tappert, and C. G. Wolf. Online Run-On Character Recognition: Design and Performance.Internat. J. Pattern Recognition Artificial Intelligence,5 (1991), 123–137.

Guigó, R., S. Knudsen, N. Drake, and T. Smith. Prediction of Gene Structure.J. Mol. Biol.,226 (1992), 141–157.

Hecht, M. S., and J. D. Ullman. A Simple Algorithm for Global Dataflow Analysis Problems.SIAM J. Comput.,4(4) (1975), 519–532.

Hirst, S. C. A New Algorithm Solving Membership of Extended Regular Expressions. Draft.

Hopcroft, J. E., and J. D. Ullman.Introduction to Automata Theory, Languages, and Computation. Addison-Wesley, Reading, MA, 1979, Chapter 2.

Kasami, T. An Efficient Recognition and Syntax-Analysis Algorithm for Context-Free Languages. AFCRL-65-758, Air Force Cambridge Research Laboratory, Bedford, MA (1965).

Lapedes, A., C. Barnes, C. Burks, R. Farber, and K. Sirotkin. Application of Neural Networks and Other Machine Learning Algorithms to DNA Sequence Analysis. InComputers and DNA, SFI Studies in the Sciences of Complexity, vol. VII (Eds. G. Bell and T. Marr). Addison-Wesley, Redwood City, CA, 1989.

Lathrop, R. H., T. A. Webster, and T. F. Smith. Ariadne: Pattern-Directed Inference and Hierarchical Abstraction in Protein Structure Recognition.Comm. ACM,30(11) (1987), 909–921.

Lectures and Discussions. Workshop on Recognizing Genes. Aspen Center for Physics, May–June, 1990.

Myers, E. W., and W. Miller. Approximate Matching of Regular Expressions.Bull. Math. Biol.,51(1) (1989), 5–37.

Needleman, S. B., and C. D. Wunsch. A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins.J. Mol. Biol.,48 (1970), 443–453.

Sankoff, D. Matching Sequences Under Deletion/Insertion Constraints.Proc. Nat. Acad. Sci. USA,69 (1972), 4–6.

Searls, D. Investigating the Linguistics of DNA with Definite Clause Grammars.Proc. North American Conf. on Logic Programming, vol. 1, 1989, pp. 189–208.

Stormo, G. Computer Methods for Analyzing Sequence Recognition of Nucleic Acids.Rev. Biophys. Chem.,17 (1988), 241–263.

Wagner, R. A., and M. J. Fischer. The String-to-String Correction Problem.J. Assoc. Comput. Mach.,21(1) (1974), 168–173.

Wagner, R. A., and J. I. Seiferas. Correcting Counter-Automaton-Recognizable Languages.SIAM J. Comput.,7(3) (1978), 357–375.

Younger, D. H. Recognition and Parsing of Context-Free Languages in Timen 3.Inform, and Control,10(2) (1967), 189–208.