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References
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I. A. Auger and C. E. Lawrence.
Bull. Math. Biol., 51:39--54.
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D. Barrick, K. Vilanueaba, R. Kalil J. Childs, T D. Schneider, C. Lawrence,
L. Gold, and G. D. Stormo.
Quantitative analysis of ribosome binding sites in e.coli.
Nucleic Acids Research, 22(7):1287--1295, 1994.
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S. Brunak, J. Engelbrecht, and S. Knudsen.
Prediction of human mRNA donor and acceptor sites from the DNA
sequence.
Journal of Molecular Biology, 220(1):49--65, Jul 5 1991.
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R. Durbin and J.T. Mieg.
A c. elegans database.
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J. Fickett and C.S. Tung.
Assessment of protein coding measures.
Nucleic Acids Research, 20(24):6441--6450, 1992.
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David Haussler.
Private communication.
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A. Krogh, I. S. Mian, and D. Haussler.
A Hidden Markov Model that finds genes in E. coli DNA.
(UCSC-CRL-93-33), 1993.
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A. Lapedes, C. Barnes, C. Burks, R. Farber, and K. Sirotkin.
Application of neural networks and other machine learning algorithms
to dna sequence analysis.
In G. Bell and T. Marr, editors, Computers and DNA, SFI
Studies in the Sciences of Complexity, volume VII, pages 157--182.
Addison-Wesley, 1989.
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M.C. O'Neill.
Escherichia coli promoters: neural networks develop distinct
descriptions in learning to search for promoters of different spacing
classes.
Nucleic Acids Research, 20(13):3471--3477, Jul 11 1992.
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Schneider TD; Stephens RM.
Sequence logos: a new way to display consensus sequences.
Nucleic Acids Research, (20), 1990.
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K.E. Rudd.
ASM News, 59:335--341, 1993.
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D. Sankoff.
Math. Biosci., 111:279--293, 1992.
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David Searls.
The linguistics of dna.
Scientific American, pages 579--591, 1992.
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E. E. Snyder and G. D. Stormo.
Nucl. Acids Res. 21, pages 607--613, 1993.
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R. Staden.
Finding protein coding regions in genomic sequences.
Methods in Enzymology, 183:163--180, 1990.
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R. Staden and A. D. McLachlan.
Codon preference and its use in identifying protein coding regions in
long DNA sequences.
Nucleic Acids Research, 10:141--156, 1982.
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G. D. Stormo and D. Haussler.
Optimally parsing a sequence into different classes based on multiple
types of information.
August 1994.
Figure: Optimal Parse of sequence of length 8 with 1 nongene region,
followed by gene region, followed by a nongene region
Figure: Schematic Diagram of E.Coli contigs
Figure: Frequency of Occurency of Gene Lengths in Codons
David Konerding
Sun May 21 12:19:38 PDT 1995