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This article is part of the supplement: Proceedings of the Sixth Annual MCBIOS Conference. Transformational Bioinformatics: Delivering Value from Genomes

Open Access Proceedings

Exploratory visual analysis of conserved domains on multiple sequence alignments

TJ Jankun-Kelly*, Andrew D Lindeman and Susan M Bridges

Author Affiliations

Institute for Digital Biology and Department of Computer Science and Engineering, Bagley College of Engineering, Mississippi State University, Mississippi, USA

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BMC Bioinformatics 2009, 10(Suppl 11):S7  doi:10.1186/1471-2105-10-S11-S7

Published: 8 October 2009



Multiple alignment of protein sequences can provide insight into sequence conservation across many species and thus allow identification of those sections of the sequence most critical to protein function. This insight can be augmented by joint display of conserved domains along the sequences. By fusing this metadata visually, biologists can analyze sequence conservation and functional motifs simultaneously and efficiently.


We present MSAVis, a new approach combining luminance and hue for simultaneous visualization of conserved motifs and sequence alignment. Input for the algorithm is a multiple sequence alignment in a standard format. The NCBI Conserved Domain Database (CDD) is used for finding conserved domains along the alignment. The visualization quickly identifies conserved domains, and allows both macro (sequence-long) and micro (small amino-acid neighborhood) views.


MSAVis utilizes two visual cues, luminance and hue, to facilitate at-a-glance summary of the conservation of a user-provided protein alignment while enabling multiple comparisons among functional domains. These visual cues are preattentive and separable so that the relationship between conservation strength and domain membership can be understood. The MSAVis software, written in Python and using BioPython and OpenGL, can be found at webcite.