"I prefer to use Primer Premier Pro over Oligo
for my primer design because I find the interface
more intuitive and can design primers more rapidly."
-Nick Allegretto, Department of Cardiovascular Biophysics and Molecular Pharmacology, Bristol-Myers Squibb
Primer Premier 5 is powerfully featured, intuitively designed and competitively priced. It offers all the important functionality available with Oligo, but is much more intuitive and easy to use. Scientists working at prestigious companies, who were using Oligo are now converting to Primer Premier 5.
The most striking difference between the products is that Oligo searches for primers and presents the entire pool (sometimes as large as 3000 primers) to the user. The bewildered user is expected to evaluate and choose the most suitable primers from this pool, using his own insight and ingenuity without much help from the program. Primer Premier 5, on the other hand, shows only the best available primers meeting the search criteria (usually far fewer than 100) and presents them in ranked order. Users who have used the top ranked primers without any further analysis, have experienced high PCR yields.
Degeneracy: Though both programs support degenerate sequences, only Primer Premier 5 automatically searches for primers with low degeneracy. It chooses primers with low overall degeneracy, as well as paying special attention to the degeneracy at the 3 end. The parameters specifying acceptable degeneracy level are under user control. With Oligo, the only recourse left to find primers with low degeneracy is manual screening of the large pool of available primers. This is a laborious, time consuming task.
Site-Directed Mutagenesis: When designing a primer for site- directed mutagenesis, as you modify the primer base by base, Primer Premier 5 displays the restriction sites to enable you to easily incorporate or remove restriction enzyme site within the primer. This dynamic display is an invaluable tool for incorporating the desired recognition sites within the primer.
Translation: Primer Premier 5 provides several mitochondrial codon
tables along with universal codon table for protein
translation and reverse translation. In addition,
you can add new mitochondrial codon tables to the
set. Oligo is a trademark of Wojciech Rychlik.
Primer Premier is the most comprehensive software to design and analyze PCR primers.
Primer Premier's search algorithm finds optimal PCR, multiplex and SNP genotyping primers with the most accurate melting temperature using the nearest neighbor thermodynamic algorithm. Primers are screened for secondary structures, dimers, hairpins, homologies and physical properties before reporting the best ones for your sequence, in ranked order. Equipped with a handy calculator, you can easily manipulate sequences and analyze the results of your primer design.
With Primer Premier, you can load sequences from dbSNP and have the primers designed flanking the SNP selected. Hundreds of unpublished SNPs can also be loaded by specifying them as variation features in standard GenBank/dbSNP files. After specifying the SNPs, primers can be designed to amplify them for detection using a probe-based chemistry.