OLIGO Primer Analysis Software
is the essential tool for designing and analyzing sequencing and PCR primers, synthetic genes, and various kinds of probes including siRNA and molecular beacons.
Based on the most up-to date nearest neighbor thermodynamic data, Oligo's search algorithms find optimal primers for PCR, including TaqMan, highly multiplexed, consensus or degenerate primers. Multiple file batch processing is possible. It is also an invaluable tool for site directed mutagenesis.
For each primer or primer pair, Oligo's various analysis windows show a multitude of useful data, such as DNA and RNA secondary structure, dimer formation, false priming and homology, internal stability, composition and physical properties. With Oligo you can analyze open reading frames down to predicted molecular weight and pKa of proteins, and search for restriction enzyme sites, not only in DNA but also in reverse-translated proteins.
The first version of the software appeared on the market in 1989. It went through several modifications, and the last one, the change from version 6 to 7, was the most comprehensive. Oligo 7 can automatically select multiplex primers, process sequence files in batch modes, automatically design PCR primers to cover multiple DNA regions in just one search and automatically find primer/probe sets for real time PCR or finds nested primers sets. Oligo search protocols (scoring system) may be customized in detail, so you may optimize the results according to your specific needs.
Oligo runs on Macintosh and Windows and it may be downloaded from this site. Click on the Tutorials link above to see Oligo 7 general overview and the major windows screen designs.