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BMC Res Notes. 2015 Mar 7;8:70. doi: 10.1186/s13104-015-1009-z.

Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences.

Author information

1
Department of Biochemistry, University of Washington, UW Box 357350, 1705 NE Pacific St, Seattle, WA, 98195-7350, USA. djaschob@uw.edu.
2
Department of Biochemistry, University of Washington, UW Box 357350, 1705 NE Pacific St, Seattle, WA, 98195-7350, USA. tdavis@uw.edu.
3
Department of Biochemistry, University of Washington, UW Box 357350, 1705 NE Pacific St, Seattle, WA, 98195-7350, USA. mriffle@uw.edu.
4
Department of Genome Sciences, University of Washington, UW Box 357350, 1705 NE Pacific St, Seattle, WA, 98195-7350, USA. mriffle@uw.edu.

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.

FINDINGS:

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.

PMID:
25884379
PMCID:
PMC4354989
DOI:
10.1186/s13104-015-1009-z
[Indexed for MEDLINE]
Free PMC Article

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