Genomic oligonucleotide microarrays

Non-coding sequences

Protein coding

25-mers

(12% of genome)

295,936 oligonucleotides (including controls)

Intergenic regions: ~6bp spacing Genes: ~70 bp spacing

Not polyA (or 3' end) biased

Strengths: Gene family paralogs,

RNA fine structure (adjacent promoters),

untranslated & antisense RNAs, DNA-protein interactions.

Affymetrix: Mei, Gentalen,

Johansen, Lockhart(Novartis Inst)

HMS: Church, Bulyk, Cheung,

Tavazoie, Petti, Selinger

tRNAs, rRNAs

E. coli

25-mer array

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