IdeogramBrowser Software Documentation
A Java tool for visualizing genomic aberrations
using Affymetrix SNP arrays.


The IdeogramBrowser can be used to easily compare a set of output files from the Affymetrix Chromosome Copy Number Analysis Tool. Loss of heterozygosity (LOH) or loss/gain markers are plotted against their corresponding chromosomal region in a karyotypic representation together with genes.


IdeogramBrowser provides:



Known Problems

Data Flow

  1. Data Import of CNT or text file
  2. Thresholding for gain/loss or LOH detection
  3. Optional merging of two or more SNP profiles
  4. Pre- or post-merge filtering via a sliding window approach
  5. Consensus region finding
  6. Interactive exploration, SVG export
IdeogramBrowser data flow


The software requires the Java runtime environment 1.5.0 (JRE 5.0) which can be downloaded from
  1. Install JRE 5.0 (1.5.0) or newer if it is not available on your system.
  2. Download the current IdeogramBrowser version and unpack the file into a directory. MacOS X users can alternatively use the .dmg disk image.
  3. Start IdeogramBrowser by Hint: It is not recommended to call IdeogramBrowser by a direct click on the ideogram.jar file since the standard memory assignment is too low for the most file arrangements.
IdeogramBrowser is packed into a single zip archive which must be unzipped (e.g. using WinZip) into the desired directory (e.g. "C:\Program Files\" or your home directory). Call in the IdeogramBrowser directory from the command line (Linux or Mac OS X) or double click ideogram.bat under Microsoft Windows in the file explorer.
When importing many files IdeogramBrowser may report an out of memory error. In these cases open (Linux or Mac OS X) or ideogram.bat (Windows) with a text editor (e.g. vi, Emacs, or notepad) and change the memory size by editing the two -X options of the java call. The -X options specify the memory size (in MB) assigned to the software. These can be adapted depending on the available memory and the testset size (number of imported .cnt files). The standard settings are usually too small for the most problems (2MB for Sun Java 1.5 on Linux and 1MB on win). Replace the two parameters e.g. by -Xmx1024m -Xms1024m for assigning 1024MB memory to the software.


Pre-Compiled Version

The current IdeogramBrowser version can be downloaded from this link: (v0.20.4)
IdeogramBrowser-0.20.4.dmg (v0.20.4, Mac OS X) (v0.20.3) (v0.20.0) (v0.19.8) (v0.19.7) (v0.19.5)

Source Code

IdeogramBrowser-0.20.3-src.tar.gz (v0.20.3)
IdeogramBrowser-0.20.0-src.tar.gz (v0.20.0)
IdeogramBrowser-0.19.8-src.tar.gz (v0.19.8)
IdeogramBrowser-0.19.7-src.tar.gz (v0.19.7)


Creative Commons License
This work is licensed under a Creative Commons Attribution 2.5 License.
Please cite the paper:
Mueller A, Holzmann K, Kestler HA, Visualization of genomic aberrations using Affymetrix SNP arrays, Bioinformatics, 23(4):496-497, 2007

Included Libraries

IdeogramBrowser includes the following open source Java libraries:

Running IdeogramBrowser

The following steps lead to a chromosomal displayed marker set:
  1. Import a marker set
  2. Filtering (Choose copy number value and threshold)
  3. Explore the displayed ideogram

Import File Formats

IdeogramBrowser can import two different file formats:

Tabbed Text File Format

This is a tab delimited ASCII file format with one aberration value in each line which can easily be generated by e.g. Microsoft Excel or OpenOffice.

Each marker line should contain five columns:
START_BP (Integer > 0)
STOP_BP (Integer > 0)
NAME (String)
VALUE (Integer)
A short example can be downloaded: marker_example.txt. The VALUE field represents a copy number which is defined by the following ranges:
VALUE < 0Illegal value
0 < VALUE < 2Loss
2No aberration
VALUE > 2Gain

CNAT Export File Format

IdeogramBrowser can import the Affymetrix Chromosome Copy Number Analyis Tool (CNAT) output file format (.cnt files). The tab-delimited TXT format of the CNAT tool is currently not supported. A brief summary of using CNAT to generate these files is given in the CNAT manual. Example files can be downloaded: Affymetrix sample data sets (these have to be first processed by CNAT 3.0 or newer to compute the copy numbers). The Affymetrix example data sets MCF7, Ref103, SKBR3, and ZR75-30 were processed by CNAT 3.0 with the standard settings and the corresponding CNT files can be downloaded

Importing Input Files

Tabbed Text File

Choose the menu point Load Markers in the File menu and navigate to a file in the format described in text file format.

CNAT Export File

Choose the menu point Load Markers in the File menu and navigate to a file in the format described in CNT file format.


The imported marker sets can be thresholded and filtered. All required parameters can be controlled via the filtering panel. Upon pressing the OK button the visualization is immediately adapted.
IdeogramBrowser filtering panel
The following parameters can be adapted:
With clicking on the inv button the colors for gains/losses are switched. A click with the right mouse button on a color shows a color selector from which a customized color can be selected.
Display Modes
Condensed Mode Shows only non-empty marker lines if activated.
Show Lines Shows a gray background line for each sample
Field Selection
Depending on the loaded CNAT format version (3 or 4) different fields appear in the field selector. Using the drop down menu on the filter panel switches between the display of
CNAT 3 format
CNAT 4 format
CNState, Log2Ratio, HmmMedianLog2Ratio, NegLog10Pvalue, LOHProb
values from the CNT files. In case of tabbed text file input only copy numbers are supported and displayed (see tabbed text file format).
The imported values could be thresholded by tuning the lower and upper bounds for the copy number detection. After pressing the OK-Button all markers with values lower/greater than the lower/upper bound will be displayed in the ideogram on the left/right side of the chromosomes.
Merging Method
When merging multiple SNP files into a single profile via the context menu Merge Marker File among two different alternatives can be chosen:
Filtering Method
It can be choosen among three filtering routings: For single profiles the last two methods are identically.
Filtering Parameters
Group limit is used to restrict the view on groups of adjacent markers with the given minimal group size. Additionally a minimal length for the length of this group in million base pairs could be set. Both criteria have to be fulfilled for a certain region in order to be shown in the diagram.
Consensus Mode
If the check box Consensus Mode is activated a further marker line is shown in the diagram. Only those regions are shown for which at least n number of samples vote for gain/loss or LOH. This limit is configurable via the spin button on the right side of the consensus mode check box.

Interactive Exploration

IdeogramBrowser allows the interactive exploration of the marker sets.
IdeogramBrowser screenshot

The upper (ideogram) panel shows the 24 chromosomes and the imported markers. When moving the mouse slowly over the chromosomes, the corresponding genome region under the mouse is shown in a small tool tip window. Also the GeneID and gene names are shown when moving the mouse over the blue bar on the right side of the chromosomes.
When a gene is selected with the left mouse button the details of the selection are listed in the info panel below the ideogram panel. If a marker is selected (blinking) the marker info and a summary of intersecting genes is displayed on the info panel.

The Karyogram Panel

Depending how many datasets are loaded into IdeogramBrowser one marker line appears on the left and the right side of the ideogram. A data slot can be selected with the mouse by clicking on the gray marker line. Once a data slot is selected all SNPs (independent of the merge mode and the number of losses/gains or LOHs) are shown on the left side for an assessment of the coverage of the genome.

karyogram panel

The Info Panel

The lower (info) panel shows the information for the selected items on the ideogram panel. Marker info and/or gene info is available. Clicking on the hyperlinked gene names opens a browser window displaying additional information from the webpage.

IdeogramBrowser info panel

Tool Tip Info Window

When moving the mouse over chromosomes, genes, or markers a small tool tip window appears showing information about the chromosomal region, the genes or the SNP markers.

Popup Menu

By clicking the right mouse button on a marker/marker line the popup menu opens. It provides Zoom In and Zoom Out fields for zooming into the chromosomes. Show All shows the whole chromosome. If a marker is selected additional the Remove Marker File option is shown. By choosing this command the complete marker line containing the selected marker is removed from the workbench. The context menu item Merge marker file enables to merge the currently selected marker line with another CNT file. This feature is useful for importing split files such as those originating from the CNAT analysis of 100k chips.
IdeogramBrowser context menu

Keyboard and Mouse Commands

The ideogram panel could be controlled by clicking the folowing keys:

Saving a Karyogram

Select File/Save to save the current karyogram as JPEG, PDF, or SVG (scalable vector graphics). Hint: SVG export may take a very long time.

The original version of this page is available at


Single chromosomes or the whole ideogram can be printed via the two menu items Hint:The printing may not work under Linux in combination with CUPS - this is a Java 1.5/CUPS problem: export the diagrams as pdf and print e.g. with Acrobat reader.


The gene/ideogram database

The two database table ideogram.gz and are packed into the jar archive of IdeogramBrowser. The current version of this database are available on the NCBI ftp site: Older versions can be found in the archives Just place the above mentioned files into the ideogram/data directory in the archive (unjar and jar the archive with the manifest.txt file). As the file format of these tables changes for (nearly) every release it may be necessary to
  1. adapt the read() functions in ideogram.db.GeneDB and ideogram.db.IdeogramDB, or
  2. reformat the database files such that they have the BUILD.36.2 format.

Hans A. Kestler
© by Hans A. Kestler & André Müller