The Genome Environment Browser (GEB) is a Java application developed to visualise
distribution of genomic features in high resolution. The project is a collaboration
between the Bioinformatics Support Service, Centre
for Bioinformatics, Imperial
College London, UK and the MRC Clinical
Sciences Centre, London, UK.
GEB requires access to a MySQL database that is populated by core data from Ensembl. Further user generated annotations and microarray expression data can be added to this data. There are 2 options for using creating the core database. Perl scripts are provided to automatically build the database for any Ensembl annotated genome. This requires access to a Unix/Linux server and some knowledge of the Perl language. Alternatively we provide 3 pre-built databases for human, mouse and rat. These can be downloaded and installed into a MySQL database using a provided Java GUI. This GUI can also be used to upload user annotations and microarray data to the database.
GEB annotation for three mammalian genomes are available at the time of writing: human (NCBI Build 36),
mouse (NCBI Build 37), rat (RGSC3.4) and can be downlaoded from the "Databases" link above..
GEB is a Java program and requires at least Java 1.5.
It is provided as a platform independent (Windows, Unix/Linux or Mac) self executable file.
The program accesses a database sited at Imperial College London.
The option to build a core database requires Perl, the Ensembl Perl API and DBI modules.
GEB starts with the welcome page, where the species, chromosome of interest and features to be displayed
can be chosen by checking the relevant boxes. Histogram scale for a given feature (e.g. genes)
can also be standardised for all chromosomes viewed by selecting “across chromosomes”
for “histograms relative”.
The welcome page leads onto the first display, a histogram showing the
length of an entire chromosome on the X-axis and the copy number of each type of feature per
1Mb, 500kb or 100kb plotted on the Y-axis. The histogram display aims at providing a panoramic
view across a chromosome for spotting global patterns as well as locating specific region(s) of
interest for detailed investigation.
Select a region of interest (ranging from 500bp to 25Mb) on the histogram
view either by moving the blue navigation bar, or typing in exact chromosome bp position numbers
in the top left boxes (labelled “Chrom. Pos”), and then click the button “View”. It will then
lead onto the physical map display, which shows the selected region of interest in greater detail.
The view can be zoomed into and items selected to display feature details
GEB provides options to save selected data or the display itself. It can calculate
the copy number and/or percentage sequence representation of any type of annotated
features across a genomic region of any size. For a more detailed analysis, the
calculation can also be done in defined intervals (e.g. every 100kb) across the
region of interest.
The initial GEB development project was a collaboration between Dr. Derek Huntley (Bioinformatics Support Service, Imperial College London) and Dr.
Amy Tang (in Neil Brockdorff’s lab, Developmental Epigenetics Group, MRC Clinical Sciences Centre)