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
Major Features in Primer Not
* 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
- *Cross Species Primer Designing: Designs primers for multiple species in a highly conserved region allowing a single primer pair to amplify all sequences.
- Allele Specific Primer Designing: Designs
primers that specifically amplify a single members
of a gene family.
- Pathogen Detection: Detects highly mutagenic
pathogens by locating primers in highly conserved
- Consensus Sequence: Generates a consensus
sequence using a ClustalW alignment. Enables visualization
of primer homology to all sequences.
- Multiplex Primers from Different Targets: Analyzes a pool of primers for multiple target sequences
for cross homologies.
- Primer Rating: Primers are rated according
to amplification efficiency and presented in ranked
- Enzyme Filtering: Provides filtering of
enzymes by overhang type, recognition site length,
and overhang sequence.
- Motif Analysis: Analyzes sequence for the
presence of motifs. Allows user defined motfis.
Major Features in Oligo Not in
- LCR: Support for the ligase chain reaction.
- Multiple tm Algorithms: Display tm calculation
from older algorithmns in addition to nearest neighbor
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.