TY - JOUR
T1 - Genome Projector
T2 - zoomable genome map with multiple views.
AU - Arakawa, Kazuharu
AU - Tamaki, Satoshi
AU - Kono, Nobuaki
AU - Kido, Nobuhiro
AU - Ikegami, Keita
AU - Ogawa, Ryu
AU - Tomita, Masaru
N1 - Funding Information:
We would like to thank Kazuki Oshita for providing technical assistance for the implementation of BLAST search feature. The Roche Biochemical Pathways wall chart was provided courtesy of Roche Diagnostics GmbH, Germany. We would like to thank the ExPASy team of the Swiss Bioinformatics Institute for kindly granting the use of digital images and coordinate data from the Roche Biochemical Pathways wall chart. This research is supported by the Grant-in-Aid for Young Scientists No.19810021 and No.20710158 from the Japan Society for the Promotion of Science (JSPS), as well as funds from the Yamagata Prefectural Government and Tsuruoka City.
PY - 2009
Y1 - 2009
N2 - BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.
AB - BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.
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U2 - 10.1186/1471-2105-10-31
DO - 10.1186/1471-2105-10-31
M3 - Article
C2 - 19166610
AN - SCOPUS:62249097015
SN - 1471-2105
VL - 10
SP - 31
JO - BMC bioinformatics
JF - BMC bioinformatics
M1 - 31
ER -