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GenomeViz Home Page
Visualizing Microbial Genomes Download GenomeViz
New Version 1.2!
New: See GenomeViz on Cover of PLoS Computational Biology !
GenomeViz
Rohit Ghai*, Torsten Hain, Trinad Chakraborty
An increasing number of microbial genomes are being sequenced and deposited in public databases. Another emerging trend is the sequencing of several closely related strains for performing genome comparisons on a finer scale. Consequently, the need for visualization of microbial genomes has also increased. GenomeViz was developed to enable rapid visualization of several prokaryotic genomes and to provide an interactive environment for microbial genome comparisons.
GenomeViz is now published in the journal BMC Bioinformatics . You can access the fulltext of the manuscript here. If you want a PDF file click here.
The figure above was contributed by Carsten Künne. See more screenshots!
Features
- Visualize classification-type data (e.g COGs classification or even your own)
- Plot numerical data (GC content, GC skew, gene expression data, sequence similarity) on color gradients or line graphs
- Plot whole genome alignments (complete or draft genomes)
- Plot upto eight different genomes in one session
- Plot two strands or only one for a genome
- Mouse-over each gene to reveal annotation
- Click, select, color and highlight genes of choice in any genome
- Search and highlight genes using regular expressions in any genome
- Create publication quality circular plots
- Over a hundred genomes available for immediate visualization
- Simple input data format, minimum customization needed
Accessory programs
tagit - PERL script which places user-defined "tags" in a map file based on your gene list.
avid2viz - PERL script which will reformat alignment data from the AVID program to map file format that can be plotted in GenomeViz. Useful for plotting whole-genome alignments in circular plots.
NEW! gc2viz - PERL script to compute GC content from a fasta formatted nucleotide sequence file of a complete genome. Creates output files ready to be plotted in GenomeViz.
NEW! gcskew2viz - PERL script to compute GC/AT skew from a fasta formatted nucleotide sequence of a complete genome. Creates output files ready to be plotted in GenomeViz.
Keep checking this page for more GenomeViz scripts that will be released soon! And if there is request for some specific script please write to us.
If you have developed a script/program for formatting data before plotting data in GenomeViz and would like to share it with other GenomeViz users, please get in touch, we would be glad to put it up on this home page so your work benefits all GenomeViz users!
Tcl Regular Expressions
A complete guide to tcl regular expression syntax can be found here.
Supported Operating systems
GenomeViz works only on unix-based platforms. Linux, Solaris and Unix should work fine.
We have tested GenomeViz on Linux (RedHat, Fedora, Debian) and Solaris systems. .Requirements
GenomeViz is written in ActiveTcl from ActiveState . This can be freely downloaded from http://tcl.activestate.com. Though a windows version for ActiveTcl is also available, due to a bug in the windows library which causes small arcs to be drawn incorrectly, GenomeViz works only on unix-based platforms. GenomeViz is not currently tested on Macintosh.
The PERL scripts will run easily as PERL is usually already installed on unix-based systems. In case you need PERL, download from http://www.perl.org or from ActiveState .How to obtain GenomeViz ?
GenomeViz is freely available for download to academic users. Commerical users must sign a commercial license agreement. See the Download page for details
Future Status
GenomeViz is under active development. Currently, pre-prepared data is available for visualizing over a hundred genomes (more than seventy genomes come with COG information). GC content analysis is also available for all genes for all these genomes. More genomes will be added soon.
Contact Information
Rohit Ghai
Institute of Medical Microbiology
Frankurter Strasse 107
35392 - Giessen
Germany
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