Genome Projector: zoomable genome map with multiple views

被引：32

作者：

Arakawa, Kazuharu ^{[1
]}

Tamaki, Satoshi ^{[1
]}

Kono, Nobuaki ^{[1
]}

Kido, Nobuhiro ^{[1
]}

Ikegami, Keita ^{[1
]}

Ogawa, Ryu ^{[1
]}

Tomita, Masaru ^{[1
]}

机构：

[1] Keio Univ, Inst Adv Biosci, Fujisawa, Kanagawa 2528520, Japan

来源：

BMC BIOINFORMATICS | 2009年 / 10卷

基金：

日本学术振兴会;

关键词：

CODON USAGE BIAS; LEADING-STRAND; SYSTEM; BROWSER; EXPASY;

D O I：

10.1186/1471-2105-10-31

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页数：10

共 45 条

[11] Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae [J].

Fukuda, Y ;

Washio, T ;

Tomita, M .

NUCLEIC ACIDS RESEARCH, 1999, 27 (08) :1847-1853

[12] PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis [J].

Gardy, JL ;

Laird, MR ;

Chen, F ;

Rey, S ;

Walsh, CJ ;

Ester, M ;

Brinkman, FSL .

BIOINFORMATICS, 2005, 21 (05) :617-623

[13] ExPASy: the proteomics server for in-depth protein knowledge and analysis [J].

Gasteiger, E ;

Gattiker, A ;

Hoogland, C ;

Ivanyi, I ;

Appel, RD ;

Bairoch, A .

NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3784-3788

[14]

Googlecom, GOOGL MAPS API

[15] Remediation of the protein data bank archive [J].

Henrick, Kim ;

Feng, Zukang ;

Bluhm, Wolfgang F. ;

Dimitropoulos, Dimitris ;

Doreleijers, Jurgen F. ;

Dutta, Shuchismita ;

Flippen-Anderson, Judith L. ;

Ionides, John ;

Kamada, Chisa ;

Krissinel, Eugene ;

Lawson, Catherine L. ;

Markley, John L. ;

Nakamura, Haruki ;

Newman, Richard ;

Shimizu, Yukiko ;

Swaminathan, Jawahar ;

Velankar, Sameer ;

Ory, Jeramia ;

Ulrich, Eldon L. ;

Vranken, Wim ;

Westbrook, John ;

Yamashita, Reiko ;

Yang, Huanwang ;

Young, Jasmine ;

Yousufuddin, Muhammed ;

Berman, Helen M. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D426-D433

[16] Towards zoomable multidimensional maps of the cell [J].

Hu, Zhenjun ;

Mellor, Joe ;

Wu, Jie ;

Kanehisa, Minoru ;

Stuart, Joshua M. ;

DeLisi, Charles .

NATURE BIOTECHNOLOGY, 2007, 25 (05) :547-554

[17] KEGG for linking genomes to life and the environment [J].

Kanehisa, Minoru ;

Araki, Michihiro ;

Goto, Susumu ;

Hattori, Masahiro ;

Hirakawa, Mika ;

Itoh, Masumi ;

Katayama, Toshiaki ;

Kawashima, Shuichi ;

Okuda, Shujiro ;

Tokimatsu, Toshiaki ;

Yamanishi, Yoshihiro .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D480-D484

[18]

Kono Nobuaki, 2006, In Silico Biology, V6, P621

[19] The UCSC Genome Browser Database: update 2009 [J].

Kuhn, R. M. ;

Karolchik, D. ;

Zweig, A. S. ;

Wang, T. ;

Smith, K. E. ;

Rosenbloom, K. R. ;

Rhead, B. ;

Raney, B. J. ;

Pohl, A. ;

Pheasant, M. ;

Meyer, L. ;

Hsu, F. ;

Hinrichs, A. S. ;

Harte, R. A. ;

Giardine, B. ;

Fujita, P. ;

Diekhans, M. ;

Dreszer, T. ;

Clawson, H. ;

Barber, G. P. ;

Haussler, D. ;

Kent, W. J. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D755-D761

[20] Chromosome evolution with naked eye: Palindromic context of the life origin [J].

Larionov, Sergei ;

Loskutov, Alexander ;

Ryadchenko, Eugeny .

CHAOS, 2008, 18 (01)

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