WebLogo 3: User's Manual

Contents

References

Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator, Genome Research, 14:1188-1190, (2004) [ Full Text ]

Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100

Creating Sequences Logos using the Web interface

Sequence Data

Enter your multiple sequence alignment or position weight matrix file, or select a file to upload. Supported file formats include CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP for multiple sequence alignments, and transfac for position weight matrices. All sequences must be the same length, else WebLogo will return an error and report the first sequence that differed in length from previous sequences.

Output format

Generally speaking, vector formats (EPS and PDF) are better for print, while bitmaps (JPEG and PNG) are more suitable for displaying on the screen or embedding into a web page.

PNG:	(600 DPI) Print resolution bitmap
PNG:	(low res, 96 DPI) Screen resolution bitmap
JPEG:	Screen resolution bitmap
EPS:	Encapsulated postscript
PDF:	Portable Document Format
SVG:	Scalable Vector Graphics

Logo size

The physical dimensions of the generated logo. Specifically, Logo Size controls the size of individual symbols stacks.

small:	5.4 points wide (same as 9pt Courier), aspect ratio 5:1
medium:	Double the width and height of small.
large:	Triple the width and height of small.

The choices have been limited to promote inter-logo consistency. Small logos can fit 80 stacks across a printed page, or 40 across a half page column. The command line interface provides greater control, if so desired.

Stacks per line

If the length of the sequences is greater than this maximum number of stacks per line, then the logo will be split across multiple lines.

Sequence Type

Selects the type of biological molecule.

auto: Automatically guess sequence type from the data

protein

dna

rna

Ignore Lower Case

Disregard lower case letters and only count upper case letters in sequences

Units

The units used for the y-axis.

probability:	Show residue probabilities, rather than information content. If compositional adjustment is disabled, then these are the raw residue frequencies.
bits:	Information content in bits
nats:	Natural units, 1 bit = ln 2 (0.69) nats
kT:	Thermal energy units in natural units (numerically the same as nats)
kJ/mol:	Thermal energy (assuming T = 300 K)
kcal/mol:	Thermal energy (assuming T = 300 K)

First position number

The numerical label of the first position in the sequence data in the input file. The label must be an integer. Residue labels for the logo will be relative to this number. (See also: Logo range.)

Logo range

By default, all sequence data from the input file is displayed in the Sequence Logo. With this option, you can instead show a subrange of the sequence data. The numbering of Start and End Positions is relative to the First Position Number. Thus, if the First Position Number is "2", Start is "5" and End is "10", then the 4th through 9th (inclusive) sequence positions of the input file will be displayed, and they will be numbered "5", "6", "7", "8", "9" and "10".

Composition

The background composition of the genome or proteome from which the sequences have been drawn. The default, automatic option is to use equiprobable background for nucleic acids and a typical amino acid usage pattern for proteins. However, you may also explicitly set the expected CG content for nucleic acid sequences, insist on equiprobable background distributions, or turn off composition adjustment altogether.

Compositional adjustment has two effects. First, the information content of a site is defined as the relative entropy of the monomers at that site to the background distribution. Consequentially, rare monomers have higher information content (when they occur) than relatively common monomers.

Secondly, the background composition is used in the small sample correction of information content. Briefly, if only a few sequences are available in the multiple sequence alignment, then sites typically appear more conserved than they really are. Small samples bias the relative entropy upwards. To compensate, we add pseudocounts to the actual counts, proportional to the expected background composition. These pseudocounts smooth the data for small samples, but become irrelevant for large samples. The proportionality constant is set to 4 for nucleic acid sequences, and 20 for proteins (these numbers have been found to give reasonable results in practice).

Behind the scenes, things are more complex. We do a full Bayesian calculation, starting with explicit Dirichlet priors based on the background composition, to which we add the data and then calculate both the posterior mean relative entropy (the stack height) and Bayesian 95% confidence intervals for error bars. These interesting details will be explained elsewhere.

Scale stack width

Scale the visible stack width by the fraction of symbols in the column.(I.e. columns with many gaps or unknown residues are narrow.)

Error bars

Display error bars. These indicate an approximate Bayesian 95% confidence interval.

Title

Give your logo a title.

Figure label

An optional figure label, added to the top left (e.g. '(a)').

X-axis

Add a label to the x-axis, or hide axis altogether.

Y-axis

The vertical axis indicates the information content of a sequence position. Use this option to toggle the y-axis and override the default axis label.

Y-axis scale

The height of the y-axis in designated units. The automatic option will pick reasonable defaults based on the sequence type and axis unit.

Y-axis tic spacing

The distance between major tic marks on the y-axis.

Sequence end labels

Choose this option to label the 5' & 3' ends of nucleic acid or the N & C termini of amino acid sequences.

Version fineprint

Toggle display of the WebLogo version information in the lower right corner. Optional, but we appreciate the acknowledgment.

Auto:

Use Base Pairing for nucleic acids (NA), Hydrophobicity for amino acids (AA).

Monochrome:

All symbols black

Base Pairing
(NA default):

2 Watson-Crick hydrogen bonds	TAU	dark orange
3 Watson-Crick hydrogen bonds	GC	blue

Classic (NA):

G	orange
TU	red
C	blue
A	green

WebLogo (version 1 and 2) and makelogo default color scheme for nucleic acids: G, orange; T & U, red; C, blue; and A, green.

Hydrophobicity
(AA default):

Hydrophilic	RKDENQ	blue
Neutral	SGHTAP	green
Hydrophobic	YVMCLFIW	black

Chemistry (AA):

Color amino acids according to chemical properties.

Polar	G,S,T,Y,C	green
Neutral	Q,N	purple
Basic	K,R,H	blue
Acidic	D,E	red
Hydrophobic	A,V,L,I,P,W,F,M	black

WebLogo (version 1 and 2) and makelogo default color. (Note that the WebLogo 2 documentation erroneously lists Q and N under green.)

Charge (AA) :

Positive	KRH	blue
Negative	DE	red

Custom:

A custom color scheme can be specified in the input field below. Specify colors on the left and associated symbols on the right. Colors are entered using CSS2 (Cascading Style Sheet) syntax. (E.g. 'red', '#F00', '#FF0000', 'rgb(255, 0, 0)', 'rgb(100%, 0%, 0%)' or 'hsl(0, 100%, 50%)' for the color red.)

More Options

The weblogo command line client, weblogo, provides many more options and greater control over the final logo appearance.