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This article is part of the supplement: EADGENE and SABRE Post-analyses Workshop

Open Access Research

IMAD: flexible annotation of microarray sequences

Dennis Prickett* and Michael Watson

Author Affiliations

Bioinformatics Group, Institute for Animal Health (IAH), Compton, Newbury, RG20 7NN, UK

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BMC Proceedings 2009, 3(Suppl 4):S2  doi:10.1186/1753-6561-3-S4-S2

Published: 16 July 2009

Abstract

Background

Accurate and current functional annotation of microarray probes is essential for the analysis and interpretation of the biological processes involved. As gene structures and functional annotation are updated in genome databases, the annotation attached to microarray probes must be updated so that scientists have access to the latest information with which to analyse their data.

Results

We have designed a pipeline and database for the annotation of microarray probes using publically available databases. The pipeline is based on NCBI BLAST, Perl and MySQL. The pipeline was used to annotate a subset of 791 differentially expressed ArkGenomics chicken probes from an experiment involving chickens infected with the protozoan parasite Eimeria. Using our pipeline, 770 of the probes were assigned at least one entry in either the Ensembl, UniGene or the DFCI gene indices databases.

Conclusion

The pipeline described here provides a simple and robust way of maintaining up-to-date and accurate annotation for microarray probes. The pipeline is designed in such a way as to be flexible and easy to update with new information.