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IMAD: flexible annotation of microarray sequences

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    Rights statement: © 2009 Prickett and Watson; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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http://www.biomedcentral.com/1753-6561/3/S4/S2
Original languageEnglish
Pages (from-to)S2
JournalBMC Proceedings
Volume3
Issue numberSuppt. 4
DOIs
Publication statusPublished - 2009
EventEADGENE and SABRE Post-analyses Workshop - Lelystad, Netherlands
Duration: 12 Nov 200814 Nov 2008

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.

Event

EADGENE and SABRE Post-analyses Workshop

12/11/0814/11/08

Lelystad, Netherlands

Event: Workshop

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