smalllogobar LogoBar smalllogo

by Åsa Pérez-Bercoff, Johan Koch, Thomas R. Bürglin.  Copyright reserved for LogoBar and its code.

LogoBar is a Java application to display protein sequence logos.
With this application you can generate protein sequence logos from multiple sequence alignments
on your own computer, and you will get an additional output file that shows the amino acid incidence
at every position of the multiple sequence alignment.

Features of the program:
    - the frequency of the residues at particular positions is represented with colored bars.
    - amino acids can be placed into groups (e.g., to have similar amino acids in the same group) according
      to the users own choice.

    - bars can be sorted according to groups, so similar amino acids will be placed together in the bar graph.
    - gaps are taken into account and also displayed in the logo.
    - Parameter changes on a loaded multiple sequence alignment
are visualized quickly since LogoBar is
      a Java application running on your local computer.

Citing LogoBar:  A paper describing LogoBar is published in the journal "Bioinformatics".
Pérez-Bercoff, Å., Koch, J. and Bürglin, T.R. (2006)
LogoBar: bar graph visualization of protein logos with gaps.
Bioinformatics 22, 112-114.
Please cite the paper when you use LogoBar to create sequence logos for your research and publications.

Download LogoBar
Sample files & examples
Detailed features

To Bürglin Lab Home Page
Other Software

Download LogoBar software

Compressed executable for Mac Os X

This is a double-clickable application that runs in Mac Os X. It requires Java 1.4.2, so should run on Mac Os X 10.3 and 10.4
Note: the "File Open" dialog behaves like in a unix environment, not like MacOsX.

Jar files for any computer system

In order to run Java software on your computer JVM (Java Virtual

Machine) has to be installed on the computer. This can be downloaded
for free at Sun's web pages at

These versions are from 20.4.2006

Zipped package: LogoBar-0.91, This version requires Java 1.4
Zipped package: LogoBar-0.912, This version requires Java 1.5

Alternatively, download the two jar files (LogoBar.jar and epsgraphics.jar) to your
and place them in the same directory. This version requires Java 1.4

The Java EPS Graphics2D package (epsgraphics.jar) package is developed by Paul Mutton and is available under the GNU general public license.

To run LogoBar, open a terminal window, move to the directory with the LogoBar.jar file and type:
java -jar LogoBar.jar

See also the README file.

Detailed features

- Assign residues to particular groups. 21 groups are available (20 amino acids and 1 gap).
  Each group can be assigned to a color. For example, the small hydrophobic residues I, V, L, M can be assigned to a group
  that gets the color green. Several different default color assignments are provided. User created groups and colors
  can also be saved.
- A floating windows shows a color legend indicating how amino acids are assigned to groups and colors.
  Clicking on the color block opens a color selection dialog.
- Bars in the graph can be sorted according to color groups. Note: gaps will always be treated separately.
- Gaps can be placed at the top or the bottom of the bars.
- Increase/decrease the vertical size of the bars (zooming in/out).
- Increase/decrease the font size for the characters placed into the bars.
- Longer sequence motifs can be split into blocks.
- Optionally turn off small number error correction.
- Optionally display the sequence logo as a traditional character-based sequence logo.
- Display residues in decreasing order of frequency under the logobar, the cut-off value can be set to a desired percentage.
- A full table with the frequency of all resides at each position is created.
- Residue lettering inside the bars can be placed within a bar either at the top or bottom.
- Bar graph sequence logo can optional display only the most conserved residue.
- Export graphs as EPS files.

Send bug reports to "thomas DOT Burglin AT biosci  DOT ki DOT se"

Last updated, 20.4.2006 by T. R. Bürglin