VAMP is a graphical user interface for the Visualization and Analysis of array-CGH, transcriptome and other Molecular Profiles. VAMP was primarily developed for visualization and analysis of tumor sample array-CGH profiles. Several types of visualization are proposed: for example classical CGH karyotype view or the genome-wide multi-tumor comparison views are available and allow the user to easily compare different arrays. Additional information concerning each clone or DNA region can be retrieved interactively from different public databases through external links. VAMP allows the user to confront the display of different types of molecular profiles such as array CGH profiles, transcriptome arrays, SNP (Single Nucleotide Polymorphism) arrays, Loss of Heterozygosity results (LOH), and Chromatin ImmunoPrecipitation arrays (ChIP chips). Many functions for analyzing CGH or other data are provided within the interface, including looking for recurrent regions of alterations, confrontation of genome data with transcriptome data or clinical information, clustering, synteny visualization, ... VAMP consists of a graphical interface written in Java 1.4.2. The software retrieves information from XML files, making it easy to install it in any laboratory.
VAMP is provided with public data sets (Nakao et al., 2004; de Leeuw et al., 2004; Pollack et al., 2002; Veltman et al., 2003; Snijders et al., 2001; Douglas et al., 2004; Gysin et al., 2005; Snijders et al., 2005) as examples which can be directly used. This document describes the installation, the configuration and the main functions of VAMP.
Note that some movies present the main functions of VAMP for basic functions, data Analysis, synteny analysis; they are available at the following URL http://bioinfo.curie.fr/vamp/doc. An HTML version of this manual with full size images also available at:
http://bioinfo.curie.fr/vamp/doc/userManual/
The manual is organized as follows: