title: LogoBar: bar graph visualization of protein logos with gaps.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  LogoBar and further documentation is available at http://www.biosci.ki.se/groups/tbu/logobar/
authors.affiliation: Department of Biosciences at Novum, and Center for Genomics and Bioinformatics, Karolinska Institutet, Alfred Nobels Allé 7, SE-141 89 Huddinge, Sweden.
authors.forename: Asa
authors.initials: A
authors.lastname: Pérez-Bercoff
authors.forename: Johan
authors.initials: J
authors.lastname: Koch
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Bürglin
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D017124:Conserved Sequence; D030562:Databases, Protein; D020407:Internet; D008969:Molecular Sequence Data; D011381:Programming Languages; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D000596:Amino Acids; D011506:Proteins