PrimerPlex

PrimerPlex designs oligos for standard multiplex PCR assays and for bead-based suspension array systems such as BioPlex-200 and Luminex 100/200 based on xMAP technology. The assays are used for high-throughput SNP applications such as genotyping, pathogen detection, strain typing, and haplotyping. It is supported on both Windows and Mac.

The following oligo design options are supported:

1. Multiplex PCR Primer Design: Can design highly specific multiplex primers for standard PCR assays for up to 30 sequences.
2. Direct Hybridization Assay (DHA) Oligo Design: Can design probes for 100 individual targets in a multiplex reaction. The SNPs are located at the center to maximize discrimination.
3. ASPE Assay Oligo Design for Allele Specific Primer Extension: Can design primers for 40 individual targets in a multiplex reaction. The mutation is located at the 3' end.

The author company, PREMIER Biosoft, has supported strain differentiation multiplex xMAP assays in one of their other products, AlleleID.