Primer Premier

Primer Premier 5 Oligo™ 6 Functional Comparison

"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

Major Features in Primer Not in Oligo

  1. *Cross Species Primer Designing: Designs primers for multiple species in a highly conserved region allowing a single primer pair to amplify all sequences.

  2. Allele Specific Primer Designing: Designs primers that specifically amplify a single members of a gene family.

  3. Pathogen Detection: Detects highly mutagenic pathogens by locating primers in highly conserved regions.

  4. Consensus Sequence: Generates a consensus sequence using a ClustalW alignment. Enables visualization of primer homology to all sequences.

  5. Multiplex Primers from Different Targets: Analyzes a pool of primers for multiple target sequences for cross homologies.

  6. Primer Rating: Primers are rated according to amplification efficiency and presented in ranked order.

  7. Enzyme Filtering: Provides filtering of enzymes by overhang type, recognition site length, and overhang sequence.

  8. Motif Analysis: Analyzes sequence for the presence of motifs. Allows user defined motfis.
* Oligo attempts to do cross species primer design by false priming. This results in numerous missed primers and the inability to locate consensus primers when sequences are divergent. In our study, Oligo failed to find primers for 3 out of 4 test sets of sequences. Primer Premier failed only 1 out of 4 due to its multiple sequence alignment ability.

Major Features in Oligo Not in Primer

  1. LCR: Support for the ligase chain reaction.

  2. Multiple tm Algorithms: Display tm calculation from older algorithmns in addition to nearest neighbor calculations

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.

Highlights of Some of the Significant Differences in the Functionality Are:

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 Design for Standard PCR Assays

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.

Primer Design for SNP Genotyping Assays

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.


  • New Improved Search Algorithms
  • Automatic Sequence Retrieval
  • Automatic Homology & Template Structure Avoidance
  • Evaluate Pre-designed Primers
  • Manual Primer Search
  • Edit Template Sequence
  • Sequence View
  • Generate Report
  • Local & Desktop BLAST Options
  • Calculator
  • Data & Database Management


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