Introduction

In molecular biology, looking at reactions and behaviors of specific molecular components in microscopic levels is important as with looking at the systematic behavior of the whole. Therefore, researchers need a scalable point of view, having access to all of the microscopic, macroscopic, and mesoscopic levels of biological knowledge. Moreover, biological data is highly multi-dimensional by nature, and understanding of the data requires multiple views, layers, or projections, for example, in the levels of genome, transcriptome, proteome, and metabolome. Here we introduce Genome Projector, a searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk. Web application of Genome Projector is available here.




Software

start Genome Projector!

Click here to start Genome Projector.

Although it should be intuitive, quick usage manual is available here.

Detailed documentations, including software download/install, development API, are available here.

All data and software (including the source code) is freely available under GNU General Public License v.2.



Publication

Our manuscript describing this online resource is published by BMC Bioinformatics with the title,
"Genome Projector: zoomable genome map with multiple views".
=>Article




Browsers

this web application is tested with the following browsers:

Internet Explorer 6 or above (we recommend using IE 7, since IE6 has performance issues)
Safari 2 or above
Firefox 2 or above (Firefox 3 has a bug in handling heavy iframe, so the map may not be property displayed at the first place. Click through different organisms to correct this.)
Opera 9 or above

*We have been informed that GenomeProjector did not work on Konqueror. Please use the above browsers instead.



Documentations

Detailed documentation is available in wiki page.



Data Mapping Service

You can overlay custom information on GenomeProjector, using your experimental data, such as microarray experiments. Mapping service is available here.



Types of views

Genome Map, Circular Genome Map, Pathway Map, DNA Walk is now available at Genome Projector!



Genome Map: Local nucleotide content is shown as graphs (A: red, T: green, G: yellow, C: Blue), and CDS are marked with blue stripes, tRNA with green stripes, and rRNA with red stripes. All objects (CDS, tRNA, rRNA) are clickable to display more information. Objects shown above the colored lines are genes on direct strand, and those below are in complementary strands.

Circular Genome Map: From the outer ring in wards, genes on direct strand (pink), genes on complementary strand (yellow), tRNAs (green arrows), rRNAs (pink or orange stripes depending on the strand), GC content (brown lines), GC skew (yellow lines). Replication origin and terminus predicted from the GC skew shift points are also labeled.

Pathway Map: Roche Biochemical Pathway Wallchart. Every enzyme (in blue text) is clickable to show more detailed information.

DNA Walk: Starting from the origin (marked by white axes), each base in the genome sequence is moved one pixel in the following directions: A-UP, T-DOWN, G-RIGHT, C-LEFT.


Zoomable user interface!

Every map is zoomable, with the familiar interface of Google Map. In addition, all elements in Genome Map and Pathway Map views are clickable, even without the pins! (This function is not available in original Google Map. Only in Genome Projector!)


320 Bacteria genome

320 circular Bacteria genomes, are now available.




Keyword search

Users can search the genome with keywords, Result of the keyword search is conserved throughout the views.




Development API

Development API is available for Google Map View! Any image (in almost any format including GIF, PNG, JPEG, BMP and even SVG) of any size can be readily converted to zoomable image using generateGMap() API distributed within the G-language Genome Analysis Environment with open-source GNU General Public License. For details, see here. (For availability and documentations about G-language GAE, see here.)

Acknowledgements

Pathway map view based on the Biochemical Pathways Wallchart is available by the courtesy of Roche Diagnostics GmbH, Germany. We would like to thank the ExPASy team of Swiss Bioinformatics Institute for providing the coordinate data for the Roche Biochemical Pathways Wallchart. Genome Projector is a product of G-language Project. This project is made possible with the free API provided by Google. This research is supported in part by the Grant-in-Aid for Young Scientists from the Japan Society for the Promotion of Science (JSPS).