OligoArray is a free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. Selection is based on three major criteria: oligonucleotide melting temperature, specificity to a single target, or at least to the shortest list of possible targets and the inability to fold to form a stable secondary structure at the hybridization temperature.
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OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
Jean – Marie Rouillard, Michael Zuker and Erdogan Gulari , Nucleic Acids Research, 2003, Vol. 31, No. 12 3057-3062