ArrayOligoSelector (AOS) is an open source program developed for the purpose of systematically designing gene-specific long oligonucleotide probes for entire genomes. For each open reading frame, the program optimizes oligo selection based upon several parameters, including uniqueness, complexity, secondary structure, GC content, and 3' end proximity.
Our laboratory has used AOS to generate Plasmodium falciparum
oligonucleotide microarrays. Other labs have used AOS for a large variety of organisms, including mouse, human, worms, and yeast.
AOS also is hosted at SourceForge here.
This site contains documentation and a user-friendly how-to.
Download an excerpt from Jing's thesis describing the AOS algorithm and implementation here.
Download AOS v3.8.4