SnoopCGH Program built to visualize and compare genomic hybridization data
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compare visualize genome visualize genome genome visualization compare genomic data

SnoopCGH Description

Program built to visualize and compare genomic hybridization data SnoopCGH is a free and open source Java desktop application built for visualizing and exploring comparative genomic hybridization (CGH) data. SnoopCGH allows the user to interactively analyze several sets of data simultaneously.The input is based on a tab-, space- or comma-delimited format, containing series of log intensity values corresponding to one or more comparisons or samples.SnoopCGH provides CGH plots with unlimited zoom (in both axes) that can be explored interactively with the mouse. The use of multiple layers, that can be stacked and combined, facilitates the visualization of the data. It is possible to apply several layers to a plot in order to filter the CGH ratios or perform statistical analysis in regions of interest. Analysis methods have been implemented and enable the rapid visualization and dissection of putative structural variations (SVs).In particular, data are smoothed using an algorithm based on Haar wavelets, and islands of potential SVs are estimated using SW-Array.A powerful feature of SnoopCGH is its ability to interface with downloadable annotation files (e.g. embl) from genomic browsers, that include information on gene names and genomic features (e.g. GC content). The user has a visual representation of the annotations at the foot of the plot and can easily access detailed textual information by clicking on them or by textual searching. Direct links to the main genomic browsers are incorporated. Requirements: · Java 1.6 or later

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