ProDesign can be used to find oligonucleotide probe sets for microarray slides. The probes can be for individual sequences or for clusters of genes. This webserver accepts files up to 200 kb in size in order to minimize the running time. For larger files please download the program from this link.
ProDesign is based on the paper:
Feng, S. and E.R.M. Tillier (2007) A Fast and Flexible Approach to Oligonucleotide Probe Design for Genomes and Gene
Families. Bioinformatics doi: 10.1093/bioinformatics/btm114
The ProDesign webserver, interfaces and logo were designed and implemented by Paulo Nuin.
If you have problems running the program please contact Elisabeth Tillier. Help is available here.