UniquePrimer - a web utility for design of specific PCR primers and probes
We have developed a web-based tool for design of specific PCR primers and probes. The program allows you to enter primer sequence information as well as an optional probe, and sequence similarity searches (MegaBLAST) will be performed to see if the sequences match the same sequence entry in the specified database. If primers (and probe) match, this will be reported. The program can handle overlapping amplicons, amplification from a single primer, ambiguous bases and other problematic cases.
Nakken S, Aussedat O, Kristoffersen AB, Holst-Jensen A, Tengs T. UniquePrimer - a web utility for design of specific PCR primers and probes. Annals of Microbiology 2009 59(2):391-393.