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PMID: 19166610 Published · epublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Genome Projector: zoomable genome map with multiple views.

BMC bioinformatics ·Vol. 10 ·2009-01-23 ·Pages 31

Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M

Abstract

Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as the genome, transcriptome, proteome, metabolome, and biochemical pathways. Due to the highly multi-layer and multi-dimensional nature of biological information, software interfaces for database browsing should provide an intuitive interface that allows for rapid migration across different views and scales. The Zoomable User Interface (ZUI) and tabbed browsing have proven successful for this purpose in other areas, especially to navigate the vast information in the World Wide Web. This paper presents Genome Projector, a Web-based gateway for genomics information with a zoomable user interface using Google Maps API, equipped with four seamlessly accessible and searchable views: a circular genome map, a traditional genome map, a biochemical pathways map, and a DNA walk map. The Web application for 320 bacterial genomes is available at http://www.g-language.org/GenomeProjector/. All data and software including the source code, documentations, and development API are freely available under the GNU General Public License. Zoomable maps can be easily created from any image file using the development API, and an online data mapping service for Genome Projector is also available at our Web site. Genome Projector is an intuitive Web application for browsing genomics information, implemented with a zoomable user interface and tabbed browsing utilising Google Maps API and Asynchronous JavaScript and XML (AJAX) technology.

MeSH Terms
Computational Biology/methods Databases, Genetic Genome Genomics/methods Internet Software User-Computer Interface
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Arakawa Kazuharu
Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan. gaou@sfc.keio.ac.jp
Tamaki Satoshi
Kono Nobuaki
Kido Nobuhiro
Ikegami Keita
Ogawa Ryu
Tomita Masaru
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Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-10-31
Email
gaou@sfc.keio.ac.jp
Published
2009-01-23
Epub
2009-00-23
Pages
31
Language
English
Region
England
NLM ID
100965194
PMCID
PMC2636772
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2105-10-31 PMC Full Text View journal details
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