VisGenome:
visualization of single and comparative genome representations
Joanna Jakubowska, Ela Hunt,
Matthew Chalmers, Martin McBride, and Anna F. Dominiczak
Contact: asia@dcs.gla.ac.uk
Application
Note published
in Bioinformatics. Source
code (version 1.0). VisGenome User Manual.
Jar
files (version 1.0) developed for geneticists at the Western Infirmary in
Glasgow.
As a
default we use Ensembl version 42, however here
you can find Database version of VisGenome for the newest version of Ensembl
(version 46, currently working very slowly).
VisGenome – Single Representation. A: shows the mouse, the
rat and the human chromosomes. B: shows an overview and detail for the rat
chromosome 18.
VisGenome – Comparative Representation. A: shows chromosomes
from the mouse, the rat and the human. B contains an overview and detail for
the rat chromosome 18 and the human chromosome 5.
VisGenome
visualises single and comparative representations for
the rat, the mouse, and the human chromosomes at different levels of details.
The tool offers smooth zooming and panning which is more flexible than seen in
other browsers. It presents information available in Ensembl for single
chromosomes, as well as homologies for any two chromosomes from different
species. The application can query supporting data from Ensembl by invoking a
link in a browser.
For
impatient users we recommend the file version of VisGenome which has downloaded
data from Ensembl v.42 and is faster than the database
version of VisGenome. If you prefer the file version of VisGenome you have to
remember to download data.zip and unpack it in the same directory as the jar.
For
users who do not want to download any files we recommend Java Web Start version of VisGenome. You just click at
the link with jnlp file and connect with the server which opens VisGenome. The
file version at Java Web Start takes the data from files from the server.
Please, see that the jnlp files available in the table above have settings for
memory reservation as initial-heap-size="256M"
max-heap-size="256M". Therefore if your machine is older and
has less memory please save the jnlp file in a directory at your computer and
adjust the memory requirements in this file. Then run it.
MAC PROBLEM.
Some
Mac machines do not like the database versions for one jar for Java 1.5.
Therefore if you have a problem with running VisGenome_DatabaseVersion_1_5_OneJar.jar
at your machine you have to unjar it and run from command line as:
java -cp
main/VisGenome_DatabaseVersion.jar:lib/mysql-connector-java-5.0.5-bin.jar
UserInterface.VisGenome.
Other
VisGenome files are here.
VisGenome
can query supporting data from Ensembl by invoking a link in a browser. The
functionality is available in Single and Comparative Representations for genes
by using left mouse button and clicking on chosen gene. You can see how the
functionality is working in Comparative Representation on the video.