OligoArray computes gene specific oligonucleotides for genome-scalle oligonucleotide microarray contruction.
Three major criteria are used for selection:

• oligonucleotide melting temperature
• specificity to a single target, or at least to the shortest list of possible targets
• the inability to fold to form a stable secondary structure at the hybridization temperature.

As of version 2.1, OligoArray depends on the OligoArrayAux sofftware to predict the formation of stable secondary structures.

References:
Rouillard JM, Zuker M, Gulari E.OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res. 2003 Jun 15;31(12):3057-62.Entrez

Rouillard JM, Herbert CJ, Zuker M. OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics. 2002 Mar;18(3):486-7. Entrez.