One of the main objectives in developing FGAs was to provide a truly comprehensive probe set . Each new GeoChip version has expanded the coverage of gene variants and expands the number of genes covered (He et al., , 2010a Lu et al., 2012a) . This continued expansion is challenging as the number of gene sequences available is constantly increasing as new sequences are being submitted to public databases. While the GeoChip design pipeline 2 has an automated update feature which uses the previously selected key words and seed sequences to search the NCBI database, downloading new sequences and designing probes is still time consuming due to the sheer volume of sequences available. As such, better and faster computation systems are needed. In addition, available microarray probe density limits are rapidly being approached as the number of GeoChip probes increases. So, new methods of array construction to increase probe density are needed.