A Gallery of Sequence Logos

This is a sequence logo of Yeast TATA sites: sequence logo of 40 yeast TATA sites
Mark C. Shaner, Ian M. Blair and Thomas D. Schneider in preparation.

What is a sequence logo?

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In the gallery, you can click on each image to get a larger one. The original figures are all in PostScript. Please visit our home page for information about sequence walkers and molecular machines.

tiny sequence logo for Lambda CI and Cro sites Aligned sequences of Lambda cI and Cro and their logo (postscript). This is figure 1 of the paper Sequence Logos: A Powerful, Yet Simple, Tool. How to build the figure.

sequence logo for E.  coli ribosome binding sites 149 E. coli Ribosome binding sites (postscript). This is figure 1 of the paper Sequence Logos: A New Way to Display Consensus Sequences

sequence logo for Lambda CI and cro sites Bacteriophage Lambda cI and Cro (postscript). This is figure 2 of the paper Sequence Logos: A New Way to Display Consensus Sequences

tiny sequence logos for bacteriophage T7 RNA polymerase
sites and experimentally generated random but strongly
functional T7 RNA polymerase sites. Bacteriophage T7 RNA Polymerase Promoters (postscript). This is figure 3 of the paper Sequence Logos: A New Way to Display Consensus Sequences

sequence logo for part of the globin genes showing a
hydrophobic stretch sequence logo for aligned globin sequences using
outlined characters and the Keller color code. Globin sequence logo (postscript). (postscript for different colors) This is figure 4 of the paper Sequence Logos: A New Way to Display Consensus Sequences.

8 tiny sequence logos in an array 8 E. coli sequence logos (postscript). This is figure 6 of the paper Information Analysis of Sequences that Bind the Replication Initiator RepA Papp, P. P., D. K. Chattoraj, and T. D. Schneider. 1993. J. Mol. Biol. 233: 219-230.

Tiny sequence logos for human donor and acceptor sites Human Splice Junctions (postscript). Information about the dataset used to create these logos. This is related to figure 1 of the paper Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites

tiny sequence logo for E.  coli ribosome binding sites1055 E. coli Ribosome Binding Sites (postscript).
tiny aligned listing of some E.  coli ribosome binding
sites Partial color aligned listing of the sites. (postscript for the complete aligned listing)
ASCII aligned listing of the sites.
These sites were reported in K. E. Rudd and T. D. Schneider, Compilation of E. coli Ribosome Binding Sites, 17.19-17.45, Jeffrey H. Miller, A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1992. Information about the data set is here here.

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Tiny sequence logos for FNR and CRP Flickering two Logos

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Some Online Papers about Sequence Logos:

Primer on information theory

Sequence Logos: A New Way to Display Consensus Sequences

Sequence Logos: A Powerful, Yet Simple, Tool

Using Information Content and Base Frequencies to Distinguish Mutations from Genetic Polymorphisms in Splice Junction Recognition Sites

Sequence Logo Reference list

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Make Your Own Sequence Logos on the Web:

With Steve Brenner's WebLogo you can create your own sequence logo - just supply a Fasta format file.

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CorreLogo: An online server for 3D sequence logos of RNA and DNA alignments

Correlation logo thumbnail E. Bindewald, T. D. Schneider and B. A. Shapiro, CorreLogo: An online server for 3D sequence logos of RNA and DNA alignments, Nucleic Acids Res. 34, w405-w411, 2006.

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Logoaid, a Unix script for making sequence logos:

Shmuel Pietrokovski (pietro@sparky.fhcrc.org Fred Hutchinson Cancer Research Center Seattle WA 98104, USA fax: (206) 667 6497; He was formerly at the Structural Biology Department, Weizmann Institute of Science, 76100 Rehovot - ISRAEL fax: 972 (8) 344105 tel: 972 (8) 343367 bppietro@dapsas1.weizmann.ac.il) has made a Unix shell script for creating sequence logos. The source code is available by anonymous ftp from the US or Israel. The Biological Computing Division at the Weizmann Institute has made an example of sequence logo and the files used to create it. The examples are under the "Silicon Graphics software" on the Unix computer used by the biology departments at the Weizmann Institute in Israel.

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Protein Sequence Blocks

tiny sequence logo of part of a protein

Here are some comments by
Shmuel Pietrokovski ! pietro@sparky.fhcrc.org
Fred Hutchinson Cancer Research Center ! fax: ##1 (206) 667 5889
1124 Columbia St. Seattle, WA 98104 USA ! tel: ##1 (206) 667 4509
on this technique for looking at protein components:

"We implemented among other things a logo representation for blocks I think its great. You can check it out by choosing the Getblock option, finding some block family you like using the full indexed keyword search, returning to the getblock screen and entering that block family number in the window. There you would see the logo options."

"Each block family has a code(BL#####, # is a digit) with no special significance except being derived from the prosite family number (PS#####)."

"Each block in a block family has logo representation. In order to see a logo you first have to choose a family and then a block in it. If you don't know the family code you can use the "full indexed keyword search of Blocks Database" to find the block using keywords (globin, serine kinase, histone etc). Even if you just want to see any logo you first have to choose a block. You can try any random number but it might happen that there is no such block family. BL00027, BL00622 are some family code I happen to remember, but you might want to see a logo of a specific family (BL01033 is the globin family)."

"We described the logo option in a manuscript about the server. You can FTP it from ftp://howard.fhcrc.org/papers/BLOCKMAKER.ps.

The paper was published at

@article{Henikoff-Pietrokovski1995,
author = "S. Henikoff
 and J. G. Henikoff
 and W. J. Alford
 and S. Pietrokovski",
title = "Automated construction and graphical presentation of protein blocks
from unaligned sequences",
journal = "Gene",
volume = "163",
pages = "GC17-GC26",
year = "1995"}

To see the example of the globin family, go here.

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RNA Structure Logos

J. Gorodkin, L. J. Heyer, S. Brunak and G. D. Stormo. Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci., Vol. 13, no. 6 pp 583-586, 1997.

sequence logo showing G.  Stormo's RNA Structure Logos "The structure logo is an extension of the sequence logo by Schneider and Stephens. We have extended the standard sequence logo to cope with any prior nucleotide distribution as well as allowing for gaps in the alignments, and indicate mutual information of basepaired positions in RNA. Thus the logo is composed by a sequence part and a structure/basepair part."



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Sequence Logos of SH3 Domain Ligands

This webpage is an attempt to compile ligand sequences for SH3 domains of various proteins. It will feature the actual alignment, logos, motif, and structural complexes of binding peptide sequences isolated from combinatorial libraries.

Maintained by:

Brian Kay
Department of Biology
University of North Carolina
Chapel Hill, NC 27599-3280

Sorry - as of 2002 Feb 12 the link to http://kay02.bio.unc.edu/sh3.html is broken. Brian Kay has disappeared ... Do you know where he went?

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Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets by neural networks

Nikolaj BLOM, Jan HANSEN, Dieter BLAAS, and Soren Brunak,
Protein Science (1996), 5: 2203- 2216.

Sequence Logos were used to study protein structures determined by neural nets. The original figures were in color. The ones on the web are black and white and low quality.

color bar Logo Sequence Conservation in Ornithine Transcarbamylase (OTC)
M. Tuchman, H. Morizono, B.S. Rajagopal, R.J. Plante, and N. M. Allewell, The Biochemical and Molecular Spectrum of Ornithine Transcarbamylase Deficiency, J. Inher. Metab. Dis. 21 (Suppl 1) 1998 40-58.

color bar Prediction Tools for Protein Homology Domain-Associated Post-Translational Modifications in the RESID Database J.S. Garavelli, D.J. Miller, and G.Y. Srinivasarao, (Protein Information Resource, National Biomedical Research Foundation, Georgetown University Medical Center, Washington, DC 20007, Poster presented at the Protein Society Meeting, July 23 - 27, 1999, Boston, MA)

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Sequence Logos in George Church's Course

Biophysic101: Genomics and Computational Biology
Church Lab WWW Server
Human RNA-splice
Protein starts
Overview
8 methods for predicting regulons
AlignACE Example:
AlignACE Example:
AlignACE Example:
AlignACE Example: Final Results

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Sequence Logos in Excel

new as of 2000 July 27
@article{Delamarche2000,
author = "C. Delamarche",
title = "{Color and graphic display (CGD): programs for multiple sequence
alignment analysis in spreadsheet software}",
journal = "Biotechniques",
volume = "29",
pages = "100-4, 106-7",
year = "2000"}
The program generates logos in Excel. The software is supposed to be in the software library at BioTechniques but I could not find it as of 2000 July 27. These logos do not have the letters sorted to put the most frequent letter at the top, but I have written to Christian Delamarche (cdelam@univ-rennes1.fr) to suggest this.

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Sequence Logos for Escherichia coli Transcription Factor Binding Sites

new as of 2001 March 27



Four members of the Schneider lab stand in front of a
tree wearing colored lab coats and representing the four
bases of DNA: G (orange, Ryan Shultzaberger); A (green,
Karen Lewis); T (red, Denise Rubins); C (blue, Natalie
Bucheimer).  The colors are the standard ones used in
sequence logos.
Human Sequence Logo. From the left, it's: Ryan (G), Karen (A), Denise (T), and Elaine (C). From Karen Lewis 1998.

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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: before 1996 June 12
updated: 2011 Jul 15
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