Chromosomal analysis made easy. IdeogramBrowser is A Java tool for visualization of 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 Features:
1. Plotting of SNP markers in a karyogram (always new generated from the ideogram table of the NCBI mapview BUILD 36.2 database). See the Appendix A for changing the default database.
2. SNP array sizes of 10k, 50k, 100k, and 500k can be imported from the Affymetrix copy number analysis tool (CNAT 3 and CNAT 4) directly in the CNT file format (version 1.0 and 1.1).
3. A general tab delimited text file format can be imported for importing foreign data (e.g. generated by a spreadsheet application such as Microsoft Excel). So the software is not limited to Affymetrix SNP arrays and the Affymetrix Copy Number Analysis Tool (CNAT 3 and 4). SNP analysis can be combined e.g. with array CGH data. The new CNAT 4 format splits the LOH markers in a second file. If the files have the same prefix the LOH files are automatically load upon opening a copy number (CN) file.
4. Plotting of gene markers from a local copy of the NCBI mapview database (BUILD 36.2)
5. Batch processing/multiple file import. Merging of split files.
6. Thresholding of log2ratios, LOH (loss of heterozygosity), SPA (single point analysis copy number), and GSA (genome smoothed copy number) values for marker generation (the latter is only available for chips with more than 10k SNPs).
7. Noise reduction via filtering functionality
8. Conensus region representation.
9. Links to www.genecards.org
10. Export to JPG, SVG, and PDF format.
11. Printing functionality (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)
12. A condensed mode is included showing only profile lines with aberrations.

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

Requirements:
* Java

The license of this software is Freeware, you can free download and free use this cad software.