Abstract
BackgroundThe 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.MethodsOur 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.ResultsThe 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.
Highlights
The sequence logo is a graphical representation of a set of aligned sequences, commonly used to depict conservation of amino acid or nucleotide sequences
Visual encoding We introduce a new visual encoding, called a Sequence Diversity Diagram, for comparative analysis of multiple sequence alignments [Figure 3]
The Sequence Diversity Diagram is designed to improve the task of visual comparison between multiple sets of aligned sequences, such as protein subfamilies
Summary
The sequence logo is a graphical representation of a set of aligned sequences, commonly used to depict conservation of amino acid or nucleotide sequences 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. Its popularity among biologists stems from its simplicity and accuracy in visually communicating the motif or signature of aligned sequence by contrasting the conserved and diverse positions by the height of single letter codes. It emphasizes the most conserved positions effectively, but this visual encoding falls short for comparative analysis of multiple groups of aligned sequences. We conclude with our future work to develop an interactive visualization tool for explorative data analysis of multiple sequence alignments
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