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

被引：4
作者：
Jaschob D. [1 ]
Davis T.N. [1 ]
Riffle M. [1 ,2 ]
机构：
[1] Department of Biochemistry, University of Washington, 1705 NE Pacific St, UW Box 357350, Seattle, 98195-7350, WA
[2] Department of Genome Sciences, University of Washington, 1705 NE Pacific St, UW Box 357350, Seattle, 98195-7350, WA
来源：
BMC Research Notes | / 8卷 / 1期
基金：
美国国家卫生研究院;
关键词：
Bioinformatics; Data visualization; Feature annotation; !text type='Java']Java[!/text]Script; Sequence annotation; Sequence feature annotation; SVG;
D O I：
10.1186/s13104-015-1009-z
中图分类号：
学科分类号：
摘要：
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 3rd 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. © 2015 Jaschob et al.; licensee BioMed Central.
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共 17 条
[1]  
Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., Et al., The human genome browser at UCSC, Genome Res., 12, 6, pp. 996-1006, (2002)
[2]  
Donlin M.J., Using the Generic Genome Browser (GBrowse), Curr Protoc Bioinformatics., 9, (2009)
[3]  
Flicek P., Amode M.R., Barrell D., Beal K., Billis K., Brent S., Et al., Ensembl 2014, Nucleic Acids Res., 42, DATABASE ISSUE, pp. D749-D755, (2014)
[4]  
Skinner M.E., Uzilov A.V., Stein L.D., Mungall C.J., Holmes I.H., JBrowse: A next-generation genome browser, Genome Res., 19, 9, pp. 1630-1638, (2009)
[5]  
Hsu F., Pringle T.H., Kuhn R.M., Karolchik D., Diekhans M., Haussler D., Et al., The UCSC Proteome Browser, Nucleic Acids Res., 33, DATABASE ISSUE, pp. D454-D458, (2005)
[6]  
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Et al., The Protein Data Bank, Nucleic Acids Res., 28, 1, pp. 235-242, (2000)
[7]  
Hunter S., Jones P., Mitchell A., Apweiler R., Attwood T.K., Bateman A., Et al., InterPro in 2011: New developments in the family and domain prediction database, Nucleic Acids Res., 40, DATABASE ISSUE, pp. D306-D312, (2012)
[8]  
Harris T.W., Baran J., Bieri T., Cabunoc A., Chan J., Chen W.J., Et al., WormBase 2014: New views of curated biology, Nucleic Acids Res., 42, DATABASE ISSUE, pp. D789-D793, (2014)
[9]  
Cherry J.M., Hong E.L., Amundsen C., Balakrishnan R., Binkley G., Chan E.T., Et al., Saccharomyces Genome Database: The genomics resource of budding yeast, Nucleic Acids Res., 40, DATABASE ISSUE, pp. D700-D705, (2012)
[10]  
Garcia L., Yachdav G., Martin M.J., FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences, F1000Res, 3, (2014)
12