LogoBar

LogoBar is a Java application that displays protein sequence logos, where gaps are accounted for when calculating the information content at each residue position in a multiple alignment. The resulting logo is displayed as bars, with amino acids displayed from the bottom up in decreasing frequencies. The bars can be color-coded, gaps in the alignment can be displayed, and residues can be arranged according to their relative abundance or grouped according to user criteria.

Topic

Small molecules;Proteins;Sequence composition, complexity and repeats;Protein sites, features and motifs;Gene and protein families

Detail

  • Operation: Multiple sequence alignment;Protein sequence analysis;Sequence alignment analysis (conservation)

  • Software interface: Web user interface

  • Language: Java

  • License: GNU Lesser General Public License v3.0

  • Cost: Free

  • Version name: 0.9.x

  • Credit: Swedish Foundation for Strategic Research

  • Input: -

  • Output: -

  • Contact: thomas.Burglin@biosci.ki.se

  • Collection: -

  • Maturity: -

Publications

  • LogoBar: bar graph visualization of protein logos with gaps.
  • Pérez-Bercoff A, et al. LogoBar: bar graph visualization of protein logos with gaps. LogoBar: bar graph visualization of protein logos with gaps. 2006; 22:112-4. doi: 10.1093/bioinformatics/bti761
  • https://doi.org/10.1093/bioinformatics/bti761
  • PMID: 16269415
  • PMC: -

Download and documentation

< Back to DB search