SeeGH--a software tool for visualization of whole genome array comparative genomic hybridization data

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Array comparative genomic hybridization (CGH) is a key technique for detecting DNA copy number variations.
• Advancements in genome sequencing and array technology enable high-resolution, genome-wide copy number analysis.
• Visualizing array CGH data requires reassembling individual data points into comprehensive chromosome profiles.

Purpose of the Study:

• To develop a novel software tool for visualizing whole genome array CGH data.
• To translate array CGH signal ratio data into high-resolution chromosome profiles.
• To facilitate the precise localization of genetic alterations through enhanced data visualization.

Main Methods:

• Developed SeeGH, a software application for array CGH data visualization.
• Data import from tab-delimited text files generated by standard microarray analysis software.
• Graphical display of data in a conventional CGH karyotype format with magnification and annotation features.
• Database integration for processing signal ratios, calculating averages and standard deviations, and linking to chromosomal regions.

Main Results:

• SeeGH successfully translates array CGH spot signal ratio data into high-resolution chromosome profiles.
• The software provides a conventional CGH karyotype diagram with options for magnification and DNA segment annotation.
• Users can hide or flag DNA segments and retrieve detailed annotation information, including clone name, sequence accession number, ratio, and chromosomal position.

Conclusions:

• SeeGH is a novel software tool for viewing and analyzing array CGH data.
• It offers both a global genomic view and magnified regional views for precise genetic alteration localization.
• The software is easily installed and compatible with Microsoft Windows 2000 and later operating systems.