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2

G. P. Dimri, K. E. Rudd, M. K. Morgan, H. Bayat, and G. F.-L. Ames. Physical mapping of repetitive extragenic palindromic sequences in and phylogenetic distribution among strains and other enteric bacteria. Journal of Bacteriology, 174(14):4583-4593, July 1992.

3

E. Gilson, W. Saurin, D. Perrin, S. Bacheullier, and M. Hofnung. Palindromic units are part of a new bacterial interspersed mosaic element (BIME). Nucleic Acids Research, 19(7):1375-1383, 1991.

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A. Krogh, I. S. Mian, and D. Haussler. A hidden Markov model that finds genes in DNA. Technical Report UCSC-CRL-93-33, University of California at Santa Cruz, Computer Science, UC Santa Cruz, CA 95064, 1993. In preparation.

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T. Kunisawa and M. Nakamura. Identification of regulatory building blocks in genome. Protein Sequences and Data Analysis, 4:43-47, 1991.

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8

A. Milosavljevic. Discovering sequence similarity by the algorithmic significance method. In Proceedings, 1st International Conference on Intelligent Systems for Molecular Biology, pages 284-291, Menlo Park, 1993.

9

A. B. Oppenheim, K. E. Rudd, I. Mendelson, and D. Teff. Integration host factor binds to unique class of complex repetitive extragenic DNA sequences in . Molecular Microbiology, 10(1):113-122, 1993.

10

G. J. Phillips, J. Arnold, and R. Ivarie. Mono- through hexanucleotide composition of the genome: a Markov chain analysis. Nucleic Acids Research, 15(6):2611-2626, 1987.

11

L. R. Rabiner. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE, 77(2):257-286, Feb. 1989.

12

K. E. Rudd. Maps, genes, sequences, and computers: An case study. ASM News, 59:335-341, 1993.

13

K. E. Rudd, 1994. Personal communication.

14

E. E. Stückle, C. Emmrich, U. Grob, and P. J. Nielsen. Statistical anlysis of nucleotide sequences. Nucleic Acids Research, 18(22):6641-6647, 1990.