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Bioinformatics Advance Access published online on November 3, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti761
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 22, 2005
Revised October 27, 2005
Accepted November 2, 2005

Applications note

LogoBar: bar graph visualization of protein logos with gaps

Åsa Pérez-Bercoff 1 #, Johan Koch 2 #, and Thomas R. Bürglin 2*

1 Dept. of Biosciences at Novum, and Center for Genomics and Bioinformatics, Karolinska Institutet; Dept. of Life Sciences, Södertörns högskola, 141 89 Huddinge, Sweden; International Master's Programme in Bioinformatics, Chalmers University of Technology, Gothenburg, Sweden
2 Dept. of Biosciences at Novum, and Center for Genomics and Bioinformatics, Karolinska Institutet; Dept. of Life Sciences, Södertörns högskola, 141 89 Huddinge, Sweden

* To whom correspondence should be addressed.
Thomas R. Bürglin, E-mail: thomas.burglin{at}biosci.ki.se


  Abstract

Summary: LogoBar is a Java application to display protein sequence logos. In our software gaps are accounted for when calculating the information content present at each residue position in a multiple alignment. The resulting logo is displayed as a graph consisting of bars, although traditional letter representation is also possible. Amino acids are displayed from the bottom up with decreasing frequencies i.e. the most abundant residue is placed at the bottom of the logo. The bars can be color-coded according to user specifications. Gaps in the alignment are also displayed, either on top or at the bottom of the logo. Furthermore, residues can either be arranged according to their relative abundance or grouped according to user criteria to emphasize the conserved nature of particular positions.

Availability: LogoBar and further documentation is available at http://www.biosci.ki.se/groups/tbu/logobar/.

# these authors contributed equally
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