Caryoscope

Caryoscope visualizes array comparative genome hybridization (aCGH) microarray data in a genomic context to display DNA copy-number changes such as chromosomal deletions and amplifications.

Key Features:

• Data Compatibility: Reads General Feature Format (GFF) files and comma- and tab-delimited files that define the genomic positions of microarray reporters.
• Genomic Visualization: Produces graphical representations that map aCGH values to genomic coordinates and chromosomes.
• Export Capabilities: Exports graphical representations to graphic formats including PostScript.
• Implementation: Implemented as a Java application.

Scientific Applications:

• Chromosome mapping: Maps microarray data onto chromosomes to identify regions of chromosome loss or duplication.
• Cancer genomics: Identifies chromosomal deletions and amplifications in tumor genomes to study DNA copy-number alterations and genomic instability.

Methodology:

Parses General Feature Format (GFF) and comma- and tab-delimited files that define microarray reporter genomic positions and integrates aCGH microarray values with genomic coordinates for graphical rendering and export.