Background: Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. Manufacturers typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions differing substantially from up-to-date sequence databases. Results: Here, we present the Re-Annotator, a re-annotation pipeline for microarrays. It is primarily designed for gene expression microarrays but can be adapted to other types of microarrays. The Re-Annotator is based on a custom-built mRNA reference, used to identify the positions of gene expression array probe sequences. A comparison of our re-annotation of the Human-HT12-v4 microarray to the manufacturer's annotation led to over 25% differently interpreted probes. Conclusions: A thorough re-annotation of probe information is crucial to any microarray analysis. The Re-Annotator pipeline consists of Perl and Shell scripts, freely available at (http://sourceforge.net/projects/reannotator). Re-annotation files for Illumina microarrays Human HT-12 v3/v4 and MouseRef-8 v2 are available as well.
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