title: Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences.
abstract: BACKGROUND
  Sequence feature annotations (e.g., protein domain boundaries, binding sites, and secondary structure predictions) are an essential part of biological research. Annotations are widely used by scientists during research and experimental design, and are frequently the result of biological studies. A generalized and simple means of disseminating and visualizing these data via the web would be of value to the research community.
  
  
  RESULTS
  Mason is a web site widget designed to visualize and compare annotated features of one or more nucleotide or protein sequence. Annotated features may be of virtually any type, ranging from annotating transcription binding sites or exons and introns in DNA to secondary structure or domain boundaries in proteins. Mason is simple to use and easy to integrate into web sites. Mason has a highly dynamic and configurable interface supporting multiple sets of annotations per sequence, overlapping regions, customization of interface and user-driven events (e.g., clicks and text to appear for tooltips). It is written purely in JavaScript and SVG, requiring no 3(rd) party plugins or browser customization.
  
  
  CONCLUSIONS
  Mason is a solution for dissemination of sequence annotation data on the web. It is highly flexible, customizable, simple to use, and is designed to be easily integrated into web sites. Mason is open source and freely available at https://github.com/yeastrc/mason.
authors.affiliation: Department of Biochemistry, University of Washington, UW Box 357350, 1705 NE Pacific St, Seattle, WA, 98195-7350, USA. djaschob@uw.edu.
authors.forename: Daniel
authors.initials: D
authors.lastname: Jaschob
authors.affiliation: Department of Biochemistry, University of Washington, UW Box 357350, 1705 NE Pacific St, Seattle, WA, 98195-7350, USA. tdavis@uw.edu.
authors.forename: Trisha N
authors.initials: TN
authors.lastname: Davis
authors.affiliation: Department of Biochemistry, University of Washington, UW Box 357350, 1705 NE Pacific St, Seattle, WA, 98195-7350, USA. mriffle@uw.edu.|Department of Genome Sciences, University of Washington, UW Box 357350, 1705 NE Pacific St, Seattle, WA, 98195-7350, USA. mriffle@uw.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Riffle
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D030541:Databases, Genetic; D033181:Information Dissemination; D020407:Internet; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009696:Nucleic Acids / Q000737:chemistry / Q000235:genetics*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D012984:Software; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D009696:Nucleic Acids; D011506:Proteins; D014157:Transcription Factors