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Bioinformatics Advance Access originally published online on November 3, 2005
Bioinformatics 2006 22(1):112-114; 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

LogoBar: bar graph visualization of protein logos with gaps

Åsa Pérez-Bercoff 1,2,3,{dagger}, Johan Koch 1,2,{dagger} and Thomas R. Bürglin 1,2,*

1Department of Biosciences at Novum, and Center for Genomics and Bioinformatics, Karolinska Institutet Alfred Nobels Allé 7, SE-141 89 Huddinge, Sweden
2Department of Life Sciences, Södertörns högskola Alfred Nobels Allé 7, SE-141 89 Huddinge, Sweden
3International Master's Programme in Bioinformatics, Chalmers University of Technology Gothenburg, Sweden

*To whom correspondence should be addressed.

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/

Contact: thomas.burglin{at}biosci.ki.se

Received on June 22, 2005; revised on October 27, 2005; accepted on November 2, 2005

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