The purpose of OligoArrayDb is to provide an easy access to pre-designed oligonucleotide microarray probes for researchers who would like to make their own microarrays. The database contains pangenomic microarray probe sets (45-mer) for most of the organisms with a fully sequenced genome, especially the ones that are unlikely to be covered by commercial microarrays. If someone decided it was worthwhile sequencing a given Archae, Bacteria or Eukaryotes, then we believe it is worth including it in OligoArrayDb to promote gene expression study on this organism using oligonucleotide microarrays. Please contact us if you would like your organism of interest added in OligoArrayDb if not yet present.
We retrieved annotated genomic sequences from public databases (Genbank, Ensembl, TIGR-JCVI) and used the latest version of the OligoArray software (Nucleic Acids Research, 2003, Vol. 31, No. 12 3057-3062 and Rouillard J.-M., unpublished data) to design probes targeting coding sequences (CDS or mRNA depending the source). Probe specificity is computed at the transcriptome level by predicting putative cross-hybridization with other transcript sequences using a thermodynamic model. Design parameters are tailored to each genome to take in account sequence properties like GC content. These parameters are accessible from each organism page. Probe design accuracy has been tested at transcriptome scale by co-designing probes targeting two organisms and hybridizing the resulting microarrays with aRNA samples derived from each organism. Here are the results and some details on the experiment design.
The content of this database is freely available. Just click on an organism name in the table below to get access to more specific details about the available probes and retreive the full set. If necessary, you can also download flat files as well as script to generate a local database.
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Organism inserted into the database during the last 30 days. 
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Dataset modified during the last 30 days