Secondary structures of primers, hairpin loops, dimers, false priming sites and cross dimers are analyzed. Search parameters can be adjusted manually, or the search may be run in automatic mode. The automatic search finds primers using stringent criteria, then gradually relaxing the stringency, until the best primers are located. As each base is changed, the program instantly calculates all relevant properties including secondary structures, melting temperature, restriction enzyme sites and amino acid translation, allowing easy addition or deletion of restriction enzyme sites and design of mutagenic primers. The protein sequence can be reverse-translated using any codon table to a degenerate DNA sequence.
Program can automatically search for primers in the region of lowest degeneracy.
Separate controls for the total percent of ambiguous bases and 3 end degeneracy maximize the amplification efficiency. Database also generates easily customized forms for oligo synthesis. Primer Premier is accompanied by a well-written and self explanatory manual.