Sequence Logos: A New Way to Display Consensus Sequences

Sequence logo of LexA binding sites

Citations to sequence logo papers per year. blue: logo paper (from 1991 to present) green: weblogo paper (from 2004 to present) red: both papers (from 1991 to present, top curve) The data are from the ISI Web of Science's Cited Reference Search. Total growth is exponential to at least 2010, but citations to the original logo paper leveled out starting in 2004 when Weblogo became available. The total may be leveling out by 2015.

@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 = "\url{http://dx.doi.org/10.1093/nar/18.20.6097},
\url{https://alum.mit.edu/www/toms/papers/logopaper/}",
year = "1990"}

• Pubmed link.
• Nucleic Acids Research page.
• Manuscript PDF version of the paper logopaper.

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

• 50th as of 05/02/2006
• 45th as of 12/11/2007 16:38:22
• 34th as of 04/16/2009 09:17:54
• 32nd as of 2010Jun19_17:45:56
• 31st as of October 1, 2010
• 29th as of March 07, 2012
• 28th as of April 20, 2012
• 27th as of May 10, 2014

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!

Programs

• makelogo - the original program. As part of the Delila system of programs, it requires other programs to create the input data.
  How Can I Make Sequence Logos on My Own Computer?
• correlogo - 3D sequence logos!
• Weblogo 2 - uses makelogo to create a web interface Be sure to read Recommendations for Making Sequence Logos
• Weblogo 3 - python version web interface Be sure to read Recommendations for Making Sequence Logos
• seqLogo - program for the R language
• GENIO/logo RNA/DNA & Amino Acid Sequence Logos by Niels Mache
• CodonLogo: a sequence logo-based viewer for codon patterns
• RILogo: visualizing RNA-RNA interactions
• BlockLogo: visualization of peptide and sequence motif conservation
• PoreLogo: PoreLogo is an automated tool for the visualization of sequence and conservation of pore-lining residues in transmembrane protein structures.
• TRX-LOGOS (DOI): DNA information content dependent upon backbone dynamics in addition to base sequence
• Skylign: "Skylign is a tool for creating logos representing both sequence alignments and profile hidden Markov models. Submit to the form on the right in order to produce (i) interactive logos for inclusion in webpages, or (ii) static logos for use in documents." PMID: 24410852
• ggseqlogo: a versatile R package for drawing sequence logos PMID: 29036507 Wagih, 2017.

Citations

• Cover of FEBS for the paper Bottger P, Pedersen L., FEBS J. 2005 Jun;272(12):3060-74. PMID: 15955065

Questions

• Questions about sequence logos at BioStar Bioinformatics Answers

Contest!

• Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests

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

Schneider Lab
origin: 1996 Feb 09
updated: 2024 Jul 09: update reference