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\newblock Protein-{DNA} interactions in regulation of {P1} plasmid replication.
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\bibitem[Barrett {\em et~al.}, 1991]{Barrett.Sober1991}
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\newblock {Against Consensus}.
\newblock {\em Syst. Zool.} {    40}, 486--493.

\bibitem[Barrett {\em et~al.}, 1993]{Barrett.Sober1993}
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\newblock {Crusade? A Reply to Nelson}.
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\bibitem[Basharin, 1959]{Basharin1959}
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\newblock On a statistical estimate for the entropy of a sequence of
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\bibitem[Box, 1979]{Box1979}
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\newblock Robustness is the strategy of scientific model building.
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\bibitem[Cheng {\em et~al.}, 1993]{Cheng.Kumar1993}
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\newblock Crystal structure of the {HhaI} {DNA} methyltransferase complexed
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\bibitem[Day \& McMorris, 1992]{Day.McMorris1992}
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\newblock Critical comparison of consensus methods for molecular sequences.
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\bibitem[de~Queiroz, 1993]{deQueiroz1993}
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\newblock {For Consensus (Sometimes)}.
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\newblock The human mutator gene homolog {{\em MSH2\/}} and its association
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\bibitem[{H\"{u}bner} \& Arber, 1989]{Hubner1989b}
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\newblock Mutational analysis of a prokaryotic recombinational enhancer element
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\bibitem[Kendrick \& Baldwin, 1987]{Kendrick.Baldwin1987}
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\newblock Cells in temporal cortex of conscious sheep can respond
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\newblock {\em The Structure of Scientific Revolutions}.
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\newblock Mutations of a {{\em mutS\/}} homolog in hereditary nonpolyposis
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\newblock {\em Cell, } {    75}, 1215--1225.

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\bibitem[Lewin, 1997]{Lewin1997}
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\newblock {\em Genes VI}.
\newblock Oxford University Press, Oxford.

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\newblock Compilation of {{\em E. coli}} {mRNA} promoter sequences.
\newblock {\em Nucleic Acids Res.} {    21}, 1507--1516.

\bibitem[Lyakhov {\em et~al.}, 2001]{Lyakhov.Schneider2001}
Lyakhov, IG, Hengen, PN, Rubens, D  \& Schneider, TD. 2001{\emph{}}.
\newblock {The P1 Phage Replication Protein RepA Contacts an Otherwise
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\newblock {\em Nucl. Acid Res.} {    29}, 4892--4900.
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\bibitem[Miller, 1955]{Miller1955}
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\newblock Note on the bias of information estimates.
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\bibitem[Nelson, 1993]{Nelson1993}
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\newblock {Why Crusade against Consensus? A Reply to Barrett, Donoghue, and
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\newblock {\em Syst. Biol.} {    42}, 215--216.

\bibitem[Papp \& Chattoraj, 1994]{PappChattoraj1994}
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\newblock Missing-base and ethylation interference footprinting of {P1} plasmid
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\newblock {\em Nucleic Acids Res.} {    22}, 152--157.

\bibitem[Papp {\em et~al.}, 1993]{Papp.helixrepa}
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\newblock Information analysis of sequences that bind the replication initiator
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\newblock {\em J. Mol. Biol.} {    233}, 219--230.

\bibitem[Pribnow, 1975]{Pribnow1975}
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\newblock Nucleotide sequence of an {RNA} polymerase binding site at an early
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\newblock {\em Proc. Natl. Acad. Sci. USA, } {    72}, 784--788.

\bibitem[Purves {\em et~al.}, 2002]{Purves.Nundy2002}
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\newblock Why we see what we do.
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\bibitem[Rager \& Singer, 1998]{Rager.Singer1998}
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\newblock {The response of cat visual cortex to flicker stimuli of variable
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\newblock {\em Eur. J. Neurosci.} {    10}, 1856--1877.

\bibitem[Reinisch {\em et~al.}, 1995]{Reinisch1995}
Reinisch, KM, Chen, L, Verdine, GL  \& Lipscomb, WN. 1995{\emph{}}.
\newblock The crystal structure of {HaeIII} methyltransferase covalently
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\newblock {\em Cell, } {    82}, 143--153.

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\newblock Exon definition may facilitate splice site selection in {RNA}s with
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\bibitem[Roberts, 1995]{Roberts1995}
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\newblock On base flipping.
\newblock {\em Cell, } {    82}, 9--12.

\bibitem[Roberts \& Cheng, 1998]{Roberts.Cheng1998}
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\newblock {Base flipping}.
\newblock {\em Annu Rev Biochem, } {    67}, 181--198.

\bibitem[Rogan {\em et~al.}, 1998]{Rogan.Faux.Schneider1998}
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\newblock Information analysis of human splice site mutations.
\newblock {\em Human Mutation, } {    12}, 153--171.
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\bibitem[Rogan \& Schneider, 1995]{Rogan.Schneider.hmsh2.1995}
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\newblock Using information content and base frequencies to distinguish
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\newblock {\em Human Mutation, } {    6}, 74--76.
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\bibitem[Schneider, 1995]{SchneiderPrimer}
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\newblock {\em Information Theory Primer}.
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\bibitem[Schneider, 1996]{Schneider.oxyr}
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\newblock Reading of {DNA} sequence logos: prediction of major groove binding
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\newblock {\em Meth. Enzym.} {    274}, 445--455.
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\bibitem[Schneider, 1997{\em{a}}]{Schneider.ri}
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\newblock Information content of individual genetic sequences.
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\bibitem[Schneider, 1997{\em{b}}]{Schneider.walker}
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\newblock Sequence walkers: a graphical method to display how binding proteins
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\newblock {\em Nucleic Acids Res.} {    25}, 4408--4415.
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\bibitem[Schneider, 2000]{Schneider.ev2000}
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\newblock Evolution of biological information.
\newblock {\em Nucleic Acids Res.} {    28}, 2794--2799.
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\bibitem[Schneider, 2001]{Schneider.baseflip.2001}
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\newblock Strong minor groove base conservation in sequence logos implies {DNA}
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\newblock {\em Nucl. Acid Res.} {    29}, 4881--4891.
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\bibitem[Schneider, 2002]{Schneider.Zen2002}
Schneider, TD. 2002{\emph{}}.
\newblock {Consensus Sequence Zen}.
\newblock {\em Applied Bioinformatics, } {    1}, 111--119.
\newblock \htmladdnormallink {http://www.lecb.ncifcrf.gov/\~{}toms/papers/zen/}
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\bibitem[Schneider \& Mastronarde, 1996]{Schneider.Mastronarde.malign}
Schneider, TD \& Mastronarde, D. 1996{\emph{}}.
\newblock {Fast} multiple alignment of ungapped {DNA} sequences using
  information theory and a relaxation method.
\newblock {\em Discrete Applied Mathematics, } {    71}, 259--268.
\newblock http://www.lecb.ncifcrf.gov/\~{}toms/paper/malign.

\bibitem[Schneider \& Stephens, 1990]{Schneider.Stephens1990}
Schneider, TD \& Stephens, RM. 1990{\emph{}}.
\newblock Sequence logos: a new way to display consensus sequences.
\newblock {\em Nucleic Acids Res.} {    18}, 6097--6100.
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\bibitem[Schneider {\em et~al.}, 1986]{Schneider1986}
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\newblock Information content of binding sites on nucleotide sequences.
\newblock {\em J. Mol. Biol.} {    188}, 415--431.
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\bibitem[Seeman {\em et~al.}, 1976]{Seeman1976}
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\newblock Sequence-specific recognition of double helical nucleic acids by
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\newblock {\em Proc. Natl. Acad. Sci. USA, } {    73}, 804--808.

\bibitem[Shannon, 1948]{Shannon1948}
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\newblock A mathematical theory of communication.
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\bibitem[Slany \& Kersten, 1992]{Slany.Kersten1992}
Slany, RK \& Kersten, H. 1992{\emph{}}.
\newblock The promoter of the {\em tgt/sec\/} operon in {{\em Escherichia
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\newblock {\em Nucleic Acids Res.} {    20}, 4193--4198.

\bibitem[Stephens \& Schneider, 1992]{Stephens.Schneider.Splice}
Stephens, RM \& Schneider, TD. 1992{\emph{}}.
\newblock Features of spliceosome evolution and function inferred from an
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\bibitem[Verdine, 1994]{Verdine1994}
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\newblock The flip side of {DNA} methylation.
\newblock {\em Cell, } {    76}, 197--200.

\bibitem[Zheng {\em et~al.}, 1999]{Zheng.Storz.oxyrfur1999}
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\newblock {OxyR and SoxRS regulation of \emph{fur}}.
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\end{thebibliography}