Oligo

Oligo 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, Oligos 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, Oligos 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.
Oligo 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.
Users will be able to customize the search protocols (scoring system), therefore the results can be optimized depending on everyones specific necessities.System requirementsJava
Intel processors and Pentium or higher
Minimum disk space: 20 MB
Minimum RAM: 128 MB
Limitations in the unregistered versionUnregistered version would not let you select primers from your own sequence file
Creating new sequence files is disabled
Editing the entire sequence is disabled
Opening sequence files is disabled
Saving sequence files is disabled