title: Sequence Diversity Diagram for comparative analysis of multiple sequence alignments.
abstract: BACKGROUND
  The sequence logo is a graphical representation of a set of aligned sequences, commonly used to depict conservation of amino acid or nucleotide sequences. Although it effectively communicates the amount of information present at every position, this visual representation falls short when the domain task is to compare between two or more sets of aligned sequences. We present a new visual presentation called a Sequence Diversity Diagram and validate our design choices with a case study.
  
  
  METHODS
  Our software was developed using the open-source program called Processing. It loads multiple sequence alignment FASTA files and a configuration file, which can be modified as needed to change the visualization.
  
  
  RESULTS
  The redesigned figure improves on the visual comparison of two or more sets, and it additionally encodes information on sequential position conservation. In our case study of the adenylate kinase lid domain, the Sequence Diversity Diagram reveals unexpected patterns and new insights, for example the identification of subgroups within the protein subfamily. Our future work will integrate this visual encoding into interactive visualization tools to support higher level data exploration tasks.
authors.affiliation: Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium ; iMinds Medical IT, Leuven, Belgium.
authors.forename: Ryo
authors.initials: R
authors.lastname: Sakai
authors.affiliation: Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium ; iMinds Medical IT, Leuven, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Aerts