Sequence Logos: A New Way to Display Consensus Sequences

Sequence logo for 38 LexA binding sites on E.  coli DNA
covering the range from the 5' side at -10 to the 3' side
at 11.  The vertical scale is from 0 to 2 bits.  The logo
letters approximately follow a sine wave running from 1 to
2 bits with wavelength 10.6 bases because LexA binds into
two adjacent major grooves of the DNA.
Sequence logo of LexA binding sites
Graph of citations to the logo and weblogo papers versus
time is exponentional from 1991 to 2010.
Number of publications (o) citing the logo (+) or weblogo (x) papers. The data are from the ISI Web of Science's Cited Reference Search. Total growth is exponential but citations to the original paper leveled out when Weblogo became available.

@article{Schneider.Stephens1990,
author = "T. D. Schneider
 and R. M. Stephens",
title = "Sequence Logos: A New Way to Display Consensus Sequences",
journal = "Nucleic Acids Res.",
volume = "18",
pages = "6097--6100",
pmid = "2172928",
pmcid = "PMC332411",
note = "\htmladdnormallink
{http://alum.mit.edu/www/toms/paper/logo/}
{http://alum.mit.edu/www/toms/paper/logo/}",
year = "1990"}

The 50 Most-Frequently-Cited Articles in Nucl. Acids Res. -- updated monthly

Historical Note: We devised the title of this paper before we realized that a sequence logo is more than merely a way to display consensus sequences. Of course it is that, since one can read the strict consensus from the top letter at each position of the logo. But in addition one gets the frequencies and the total sequence conservation, so logos are more that just a display of consensus. It takes time to begin to think in a new way!

Recommendations for Making Sequence Logos by Tom Schneider

Programs

This is a very incomplete list of sequence logo servers and extensions to logos.

Citations

Questions

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2015 Jan 28: Google Ngram use of 'sequence logo'

This graph shows the percentage of time that the phrase 'sequence logo' appeared in books in different years using the Google Books Ngram Viewer.

color bar Small icon for Theory of Molecular Machines: physics,
chemistry, biology, molecular biology, evolutionary theory,
genetic engineering, sequence logos, information theory,
electrical engineering, thermodynamics, statistical
mechanics, hypersphere packing, gumball machines, Maxwell's
Daemon, limits of computers


Schneider Lab

origin: 1996 Feb 09
updated: 2015 Jan 28: Google Ngram use of 'sequence logo'
color bar
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