Cover of Nucleic Acids Research, December 2001

2001 December 1 issue of
Nucleic Acids Research
Copyright 2001
Oxford University Press.

baseflip: Strong Minor Groove Base Conservation in Sequence Logos implies DNA Distortion or Base Flipping during Replication and Transcription Initiation

BiBTeX reference:

@article{Schneider.baseflip.2001,
author = "T. D. Schneider",
title = "Strong Minor Groove Base Conservation in Sequence Logos
implies {DNA} Distortion or
Base Flipping during Replication and Transcription Initiation",
journal = "Nucleic Acids Res.",
volume = "29",
pages = "4881--4891",
note = "\url{https://doi.org/10.1093/nar/29.23.4881},
\url{https://alum.mit.edu/www/toms/papers/baseflip/}",
pmid = "11726698",
pmcid = "PMC96701",
year = "2001"}

Companion paper: repan3

Supplementary Data

Delila instructions for each analysis provide you with a precise way to reproduce the analysis:

gal4.inst
repa.inst
rts1.inst
dnaa.inst
p4alpha.inst
ebna1.inst
orc.inst
minusten.inst to be used in conjunction with the delila library built from Hanah Margalit's database (Eur J Biochem 1994 Aug 1;223(3):823-30 Determination of common structural features in Escherichia coli promoters by computer analysis. Lisser S, Margalit H).
sigmad.inst to be used in conjunction with the complete B. subtilus genome.

Cover Figure

The cover figure is available in several forms:

baseflipcover.ps 993960 bytes This is the original PostScript figure.
baseflipcover.pdf 80313 bytes This is the original PostScript figure converted to pdf.
NAR-23.pdf 87110 bytes This is the figure as part of the December 1, 2001 cover of Nucleic Acids Research as a pdf.
NAR2001DecCover.jpg 95620 bytes This is the figure as part of the December 1, 2001 cover of Nucleic Acids Research as a jpg.
baseflipcover.cmyk 30921924 bytes
baseflipcover.tiff 23192054 bytes
baseflipcover300.tiff 1333079 bytes
baseflipcover600.tiff 1337119 bytes
bf.tiff.gz 317971 bytes

See also the DNA figure: Numbered DNA Base Pairs

If you need background information about information theory you can explore my web site. You may find these two resources particularly useful:

Information Theory Primer, With an Appendix on Logarithms
A Glossary for Molecular Information Theory and the Delila System.
A good starting point would be the definition of a bit.

Tom Schneider

2006 Aug 4

Genome-wide identification of replication origins in yeast by comparative genomics Conrad A. Nieduszynski, Yvonne Knox and Anne D. Donaldson GENES & DEVELOPMENT 20:1874-1879, 2006.

They used sequence logos to analyze replication origins. Their results are similar to figure 5D.

2003 Jan 17: The LaTeX source for this paper is available as a template for others who would like to use the powerful free typesetting language LaTeX with Nucleic Acids Research. This is not a complete functional example, as I have not put the bibliography database, style files or figures there. Maybe someday.

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Schneider Lab
origin: 2001 Jan 22
updated: 2023 Aug 17
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