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\newblock {P1} plasmid replication. {Purification} and {DNA}-binding activity
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\newblock {\em J. Biol. Chem.} {    261}, 3548--3555.

\bibitem[Abeles {\em et~al.}, 1989]{Abeles1989}
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\newblock Protein-{DNA} interactions in regulation of {P1} plasmid replication.
\newblock {\em J. Bacteriol.} {    171}, 43--52.

\bibitem[Barrett {\em et~al.}, 1991]{Barrett.Sober1991}
Barrett, M, Donoghue, MJ  \& Sober, E. 1991{\emph{}}.
\newblock {Against Consensus}.
\newblock {\em Syst. Zool.} {    40}, 486--493.

\bibitem[Barrett {\em et~al.}, 1993]{Barrett.Sober1993}
Barrett, M, Donoghue, MJ  \& Sober, E. 1993{\emph{}}.
\newblock {Crusade? A Reply to Nelson}.
\newblock {\em Syst. Biol.} {    42}, 216--217.

\bibitem[Basharin, 1959]{Basharin1959}
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\newblock On a statistical estimate for the entropy of a sequence of
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\newblock {\em Theory Probability Appl.} {    4}, 333--336.

\bibitem[Box, 1979]{Box1979}
Box, GEP. 1979{\emph{}}.
\newblock Robustness is the strategy of scientific model building.
\newblock In {\em Robustness in Statistics}, (Launer, RL \& Wilkinson, GN,
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\newblock `ALL MODELS ARE WRONG BUT SOME ARE USEFUL' is a subheader in the
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\bibitem[Cheng {\em et~al.}, 1993]{Cheng.Kumar1993}
Cheng, X, Kumar, S, Posfai, J, Pflugrath, JW  \& Roberts, RJ. 1993{\emph{}}.
\newblock Crystal structure of the {HhaI} {DNA} methyltransferase complexed
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\newblock {\em Cell, } {    74}, 299--307.

\bibitem[Day \& McMorris, 1992]{Day.McMorris1992}
Day, WHE \& McMorris, FR. 1992{\emph{}}.
\newblock Critical comparison of consensus methods for molecular sequences.
\newblock {\em Nucleic Acids Res.} {    20}, 1093--1099.

\bibitem[de~Queiroz, 1993]{deQueiroz1993}
de~Queiroz, A. 1993{\emph{}}.
\newblock {For Consensus (Sometimes)}.
\newblock {\em Syst. Biol.} {    42}, 368--372.

\bibitem[Eagleman \& Sejnowski, 2000]{Eagleman.Sejnowski2000}
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\newblock {Motion integration and postdiction in visual awareness}.
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\newblock The human mutator gene homolog {{\em MSH2\/}} and its association
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\newblock {\em Cell, } {    75}, 1027--1038.

\bibitem[Gu\'{e}ron {\em et~al.}, 1987]{Gueron.Leroy1987}
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\newblock {A single mode of DNA base-pair opening drives imino proton
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\newblock {\em Nature, } {    328}, 89--92.

\bibitem[Hengen {\em et~al.}, 1997]{Hengen.fisinfo}
Hengen, PN, Bartram, SL, Stewart, LE  \& Schneider, TD. 1997{\emph{}}.
\newblock Information analysis of {Fis} binding sites.
\newblock {\em Nucleic Acids Res.} {    25}, 4994--5002.
\newblock \htmladdnormallink
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\bibitem[{H\"{u}bner} \& Arber, 1989]{Hubner1989b}
{H\"{u}bner}, P \& Arber, W. 1989{\emph{}}.
\newblock Mutational analysis of a prokaryotic recombinational enhancer element
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\newblock {\em EMBO J.} {    8}, 577--585.

\bibitem[Kendrick \& Baldwin, 1987]{Kendrick.Baldwin1987}
Kendrick, KM \& Baldwin, BA. 1987{\emph{}}.
\newblock Cells in temporal cortex of conscious sheep can respond
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\newblock {\em Science, } {    236}, 448--450.

\bibitem[Klima\v{s}auskas {\em et~al.}, 1994]{Klimasauskas1994}
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\newblock {HhaI} methyltransferase flips its target base out of the {DNA}
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\newblock {\em Cell, } {    76}, 357--369.

\bibitem[Kuhn, 1970]{Kuhn1970}
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\newblock {\em The Structure of Scientific Revolutions}.
\newblock The University of Chicago Press, Chicago.

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  Vogelstein, B. 1993{\emph{}}.
\newblock Mutations of a {{\em mutS\/}} homolog in hereditary nonpolyposis
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\newblock {\em Cell, } {    75}, 1215--1225.

\bibitem[Leroy {\em et~al.}, 1988]{Leroy.Gueron1988}
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\newblock {Characterization of base-pair opening in deoxynucleotide duplexes
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\newblock {\em J. Mol. Biol.} {    200}, 223--238.

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

\bibitem[Lisser \& Margalit, 1993]{Lisser1993}
Lisser, S \& Margalit, H. 1993{\emph{}}.
\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
  Inaccessible Thymine N3 Proton by DNA Distortion or Base Flipping}.
\newblock {\em Nucl. Acid Res.} {    29}, 4892--4900.
\newblock \htmladdnormallink
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\bibitem[Miller, 1955]{Miller1955}
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\newblock Note on the bias of information estimates.
\newblock In {\em Information Theory in Psychology}, (Quastler, H, ed.), pp.
  95--100, Free Press, Glencoe, IL.

\bibitem[Nelson, 1993]{Nelson1993}
Nelson, G. 1993{\emph{}}.
\newblock {Why Crusade against Consensus? A Reply to Barrett, Donoghue, and
  Sober}.
\newblock {\em Syst. Biol.} {    42}, 215--216.

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

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

\bibitem[Pribnow, 1975]{Pribnow1975}
Pribnow, D. 1975{\emph{}}.
\newblock Nucleotide sequence of an {RNA} polymerase binding site at an early
  {T7} promoter.
\newblock {\em Proc. Natl. Acad. Sci. USA, } {    72}, 784--788.

\bibitem[Purves {\em et~al.}, 2002]{Purves.Nundy2002}
Purves, D, Lotto, RB  \& Nundy, S. 2002{\emph{}}.
\newblock Why we see what we do.
\newblock {\em Amer. Sci.} {    90}, 236--243.
\newblock \htmladdnormallink
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\bibitem[Rager \& Singer, 1998]{Rager.Singer1998}
Rager, G \& Singer, W. 1998{\emph{}}.
\newblock {The response of cat visual cortex to flicker stimuli of variable
  frequency}.
\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
  complexed to {DNA}: an extrahelical cytosine and rearranged base pairing.
\newblock {\em Cell, } {    82}, 143--153.

\bibitem[Robberson {\em et~al.}, 1990]{Robberson1990}
Robberson, BL, Cote, GJ  \& Berget, SM. 1990{\emph{}}.
\newblock Exon definition may facilitate splice site selection in {RNA}s with
  multiple exons.
\newblock {\em Mol. Cell. Biol.} {    10}, 84--94.

\bibitem[Roberts, 1995]{Roberts1995}
Roberts, RJ. 1995{\emph{}}.
\newblock On base flipping.
\newblock {\em Cell, } {    82}, 9--12.

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

\bibitem[Rogan {\em et~al.}, 1998]{Rogan.Faux.Schneider1998}
Rogan, PK, Faux, BM  \& Schneider, TD. 1998{\emph{}}.
\newblock Information analysis of human splice site mutations.
\newblock {\em Human Mutation, } {    12}, 153--171.
\newblock \htmladdnormallink {https://alum.mit.edu/www/toms/paper/rfs/}
  {https://alum.mit.edu/www/toms/paper/rfs/}.

\bibitem[Rogan \& Schneider, 1995]{Rogan.Schneider.hmsh2.1995}
Rogan, PK \& Schneider, TD. 1995{\emph{}}.
\newblock Using information content and base frequencies to distinguish
  mutations from genetic polymorphisms in splice junction recognition sites.
\newblock {\em Human Mutation, } {    6}, 74--76.
\newblock \htmladdnormallink
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\bibitem[Schneider, 1995]{SchneiderPrimer}
Schneider, TD. 1995{\emph{}}.
\newblock {\em Information Theory Primer}.
\newblock \htmladdnormallink
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\bibitem[Schneider, 1996]{Schneider.oxyr}
Schneider, TD. 1996{\emph{}}.
\newblock Reading of {DNA} sequence logos: prediction of major groove binding
  by information theory.
\newblock {\em Meth. Enzym.} {    274}, 445--455.
\newblock \htmladdnormallink {https://alum.mit.edu/www/toms/paper/oxyr/}
  {https://alum.mit.edu/www/toms/paper/oxyr/}.

\bibitem[Schneider, 1997{\em{a}}]{Schneider.ri}
Schneider, TD. 1997{\emph{a}}.
\newblock Information content of individual genetic sequences.
\newblock {\em J. Theor. Biol.} {    189}, 427--441.
\newblock \htmladdnormallink {https://alum.mit.edu/www/toms/paper/ri/}
  {https://alum.mit.edu/www/toms/paper/ri/}.

\bibitem[Schneider, 1997{\em{b}}]{Schneider.walker}
Schneider, TD. 1997{\emph{b}}.
\newblock Sequence walkers: a graphical method to display how binding proteins
  interact with {DNA} or {RNA} sequences.
\newblock {\em Nucleic Acids Res.} {    25}, 4408--4415.
\newblock \htmladdnormallink
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  {https://alum.mit.edu/www/toms/paper/walker/}, erratum: NAR 26(4):
  1135, 1998.

\bibitem[Schneider, 2000]{Schneider.ev2000}
Schneider, TD. 2000{\emph{}}.
\newblock Evolution of biological information.
\newblock {\em Nucleic Acids Res.} {    28}, 2794--2799.
\newblock \htmladdnormallink {https://alum.mit.edu/www/toms/paper/ev/}
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\bibitem[Schneider, 2001]{Schneider.baseflip.2001}
Schneider, TD. 2001{\emph{}}.
\newblock Strong minor groove base conservation in sequence logos implies {DNA}
  distortion or base flipping during replication and transcription initiation.
\newblock {\em Nucl. Acid Res.} {    29}, 4881--4891.
\newblock \htmladdnormallink
  {https://alum.mit.edu/www/toms/paper/baseflip/}
  {https://alum.mit.edu/www/toms/paper/baseflip/}.

\bibitem[Schneider, 2002]{Schneider.Zen2002}
Schneider, TD. 2002{\emph{}}.
\newblock {Consensus Sequence Zen}.
\newblock {\em Applied Bioinformatics, } {    1}, 111--119.
\newblock \htmladdnormallink {https://alum.mit.edu/www/toms/papers/zen/}
  {https://alum.mit.edu/www/toms/papers/zen/}.

\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 https://alum.mit.edu/www/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.
\newblock \htmladdnormallink
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\bibitem[Schneider {\em et~al.}, 1986]{Schneider1986}
Schneider, TD, Stormo, GD, Gold, L  \& Ehrenfeucht, A. 1986{\emph{}}.
\newblock Information content of binding sites on nucleotide sequences.
\newblock {\em J. Mol. Biol.} {    188}, 415--431.
\newblock \htmladdnormallink
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\bibitem[Seeman {\em et~al.}, 1976]{Seeman1976}
Seeman, NC, Rosenberg, JM  \& Rich, A. 1976{\emph{}}.
\newblock Sequence-specific recognition of double helical nucleic acids by
  proteins.
\newblock {\em Proc. Natl. Acad. Sci. USA, } {    73}, 804--808.

\bibitem[Shannon, 1948]{Shannon1948}
Shannon, CE. 1948{\emph{}}.
\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
  coli\/}} is preceded by an upstream activation sequence that contains a high
  affinity {FIS} binding site.
\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
  analysis of the information at human splice sites.
\newblock {\em J. Mol. Biol.} {    228}, 1124--1136.
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\bibitem[Verdine, 1994]{Verdine1994}
Verdine, GL. 1994{\emph{}}.
\newblock The flip side of {DNA} methylation.
\newblock {\em Cell, } {    76}, 197--200.

\bibitem[Zheng {\em et~al.}, 1999]{Zheng.Storz.oxyrfur1999}
Zheng, M, Doan, B, Schneider, TD  \& Storz, G. 1999{\emph{}}.
\newblock {OxyR and SoxRS regulation of \emph{fur}}.
\newblock {\em J. Bacteriol.} {    181}, 4639--4643.
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\end{thebibliography}
