Genome Projector: zoomable genome map with multiple views.

Kazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa, Masaru Tomita

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)31
Number of pages1
JournalBMC Bioinformatics
Volume10
DOIs
Publication statusPublished - 2009

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Projector
Genome
Genes
Application programming interfaces (API)
Browsing
Genomics
User interfaces
User Interface
Software
Bacterial Genomes
Web Application
Metabolome
Chromosome Mapping
Intuitive
Proteome
Pathway
Licensure
Transcriptome
Documentation
Internet

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

Genome Projector : zoomable genome map with multiple views. / Arakawa, Kazuharu; Tamaki, Satoshi; Kono, Nobuaki; Kido, Nobuhiro; Ikegami, Keita; Ogawa, Ryu; Tomita, Masaru.

In: BMC Bioinformatics, Vol. 10, 2009, p. 31.

Research output: Contribution to journalArticle

Arakawa, Kazuharu ; Tamaki, Satoshi ; Kono, Nobuaki ; Kido, Nobuhiro ; Ikegami, Keita ; Ogawa, Ryu ; Tomita, Masaru. / Genome Projector : zoomable genome map with multiple views. In: BMC Bioinformatics. 2009 ; Vol. 10. pp. 31.
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