Monday, April 5, 2010

TiArA: A Virtual Appliance for the Analysis of Tiling Array Data

Background

Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis.


Methodology/Principal Findings

Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range.


Conclusions/Significance

TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian package or a virtual appliance at http://purl.org/NET/tiara.


(this Post content was reproduced from: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0009993, Via PLoS ONE Alerts: Computer Science.)