Related Experiment Videos
LogoBar: bar graph visualization of protein logos with gaps
Asa Pérez-Bercoff1, Johan Koch, Thomas R Bürglin
1Department of Biosciences at Novum, and Center for Genomics and Bioinformatics, Karolinska Institutet, Alfred Nobels Allé 7, SE-141 89 Huddinge, Sweden.
Bioinformatics (Oxford, England)
|November 5, 2005
Summary
LogoBar is a Java application for visualizing protein sequence logos. It accurately calculates information content by including gaps and offers flexible display options for residue abundance and conservation.
Area of Science:
- Bioinformatics
- Computational Biology
- Structural Biology
Background:
- Protein sequence logos are crucial for visualizing conservation patterns in multiple sequence alignments.
- Existing tools may not adequately account for gaps in information content calculation.
Purpose of the Study:
- To introduce LogoBar, a novel Java application for generating protein sequence logos.
- To enhance logo visualization by incorporating gap information into content calculations.
Main Methods:
- Developed LogoBar as a Java application.
- Implemented gap handling in information content calculation for multiple sequence alignments.
- Enabled graphical bar and traditional letter representations of logos.
Main Results:
- LogoBar generates protein sequence logos with accurate information content, considering gaps.
- The application offers customizable bar coloring and residue arrangement based on abundance or user-defined criteria.
- Both graphical and letter-based logo formats are supported, with options for gap display.
Conclusions:
- LogoBar provides an improved method for visualizing protein sequence logos by accounting for gaps.
- The software offers flexibility in representation and customization, aiding in the identification of conserved residues.