Sequence Diversity Diagram for comparative analysis of multiple sequence alignments

BMC Proceedings

Research

Jan Aerts¹  Ryo Sakai¹ 

[1] 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;

关键词: Multiple Sequence Alignment;    Configuration File;    Sequential Frequency;    FASTA File;    Sequence Logo;   

DOI  :  10.1186/1753-6561-8-S2-S9

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Sakai and Aerts; licensee BioMed Central Ltd. 2014