In the exon module, coding sequences are identified within a genomic sequence by aligning cDNA and/or EST sequences using the program Spidey. In the object definition, exons are symmetrically extended by 50 bp on both sides to include the branch point and the splicing sites. In case an excluded repeat sequence is near an exon, the exon can be extended by 25 bp or not at all. In this module, objects within a region of 250 bp are joined into one object.

The SNP module allows primer design for the validation of public SNPs. In order to map public SNPs on a given sequence, the genomic DNA is aligned to a database containing the hapmap SNPs. SNPs found within a region of 300 bp are joined into one object.

In the saturation module, the objects are the parts of the genomic sequence between the excluded. Targets are defined with a default overlap of 35 bp. Since the length of an object is not necessarily a multifold of the optimal target length, SNPbox aims to design targets approaching the optimal target length as close as possible.

This module combines the exon and saturation modules by running both sequentially