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",
comment = "baseflip.tex, journal cover!",
journal = "Nucl. Acid Res.",
volume = "29",
number = "23",
pages = "4881-4891",   
year = "2001"}

The paper is available directly from Nucleic Acids Research. No subscription required:
- Abstract: baseflip
- Full Text: baseflip
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Direct access to the paper baseflip at Nucleic Acids Research. (This requires a subscription.)
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.

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.

Schneider Lab
origin: 2001 Jan 22
updated: 2006 Aug 04