TiArA: a virtual appliance for the analysis of Tiling Array data.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 20376318.
- Also identified by DOI 10.1371/journal.pone.0009993 and PMC identifier 2848623.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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.
Medical subject headings
- Oligonucleotide Array Sequence Analysis
- Software
- User-Computer Interface