A Gallery of Sequence Logos

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

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.

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.

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

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

Bacteriophage T7 RNA Polymerase Promoters (postscript). This is figure 3 of the paper Sequence Logos: A New Way to Display Consensus Sequences

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 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.

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

1055 E. coli Ribosome Binding Sites (postscript).
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.

Flickering two Logos

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

Make Your Own Sequence Logos on the Web:

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

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.

Logoaid, a Unix script for making sequence logos:

Protein Sequence Blocks

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.

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.

"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."

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:

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?

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

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.

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.

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)

as of 2000 Jan 4

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

Sequence Logos in Excel

@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"}

Sequence Logos for Escherichia coli Transcription Factor Binding Sites

• Database
• reference: Escherichia coli Transcription Factor Binding Sites McCue, L.A., Thompson, W., Carmack, C.S., Ryan, M.P., Liu, J.S., Derbyshire, V. and Lawrence, C.E. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes NAR 2001 29:774-782. PDF

• Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR Science. 2004 Sep 17;305(5691):1743-1746. They used sequence logos to show binding sites.

Schneider Lab
origin: before 1996 June 12
updated: 2007 Nov 21