title: Exploratory visual analysis of conserved domains on multiple sequence alignments.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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 http://agbase.msstate.edu/tools/MSAVis.html.
authors.affiliation: Institute for Digital Biology and Department of Computer Science and Engineering, Bagley College of Engineering, Mississippi State University, Mississippi, USA. tjk@acm.org
authors.forename: T J
authors.initials: TJ
authors.lastname: Jankun-Kelly
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Lindeman
authors.forename: Susan M
authors.initials: SM
authors.lastname: Bridges
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins