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Nucleic Acids Research, 1983, Vol. 11, No. 7 2221-2232
© 1983

MOLECULAR BIOLOGY

Regulatory pattern Identification in nucleic acid sequences

J. R Sadler1, M. S. Waterman2 and T. F. Smith3

1Dept. Biochemistry/Biophysics/Gentics, Univ. Colorado Health Sciences Center Denver, CO 80262 2Dept. Biochemistry and Biophysics, Sch. Med., Univ. California San Francisco, CA 94121 3Theoretical Biology, Los Alamos Natl. Lab., Los Alamos, NM 87545, USA

Received September 1, 1982. Revised February 28, 1983. Accepted March 1, 1983.

In addition to the sequence homologies and statistical patterns identified among numerous genetic sequences, there are subtler classes of patterns for which most current computer search methods offer very limited utility. This class includes various presumptive eukaryotic regulatory sites. A critique of the often employed consensus and local homology methods suggests the need for new tools. In particular, such new methods should use the positional and structural data now becoming available on exactly what it is that is recognized in the DNA sequence by sequence-specific binding proteins.


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