Primo Degenerate 3.4: Degenerate PCR Primer Design
Click here for more Primo family
of PCR primer design tools.
Degenerate PCR is frequently used to clone unknown genes in a family.
Primo Degenerate 3.4 designs PCR primers based on a single peptide sequence or multiple alignments of proteins or nucleotides. For degenerate primers, the probability of binding to the target is proportional to the effective concentration of the specific primer (i.e., inversely to the fold of degeneracy). Most programs and models did not take this into account thus will predict a much too high melting temperature. By using the Nearest Neighbor Tm model, Primo automatically adjusts Tm for degenerate primers, resulting in better primer design.
See user instruction for details.
For normal PCR primer design, please use
Primo Pro 3.4 which
reduces PCR noise by lowering probability of random primering.
Primo Online runs on Java-enabled browsers|
PC: Internet Explorer 5.5 or higher and Netscape 4.08 or higher
Mac: Internet Explorer 5.0, IE5.1.4 or higher (IE5.1 will not work because of a bug.)
Need to raise a better antibody? |
Please use online Abie Pro 3.0 for
peptide antibody design.
Compare Primo to other online primer design software and find
Oligo synthesis facilities
The Electronic Protocol Book Table of contents
An electronic protocol book with 500 protocols and
100 recipes. A great quick and practical reference for bench scientists
as well as for new students. (Available for both PC and Mac.)
Get a copy
BioToolKit 300 (PC and Mac)   Order download
Primo 3.4 (PCR primer design) and Abie 3.0 (peptide antibody design)
are parts of functions included in BioToolKit 300 , a
collection of tools frequently used by bench biomedical scientists:
Primo 3.4 PCR primer design: |
Pro --- Standard PCR and RT-PCR.
Multiplex --- Multiple PCRs in one tube.
Degenerate --- Degenerate PCR for one or more genes.
Optimum --- Optimize codon usage. Gene Synthesis.
Diverse --- Most diverse regions of a family.
Unique --- Amplify one gene from a family.
MSP --- Methylation specific PCR.
Random --- Random primers for fingerprinting.
Profile --- Profile 10s-1000s of genes.
Abie Pro 3.0: Select antigenic peptide for antibody production and reduce background cross-reactions.
Centrifugation speed/force conversion for any rotor.
Molecular weight calculation for oligos, peptides, and chemicals.
Molar calculator for concentration-related calculations.
Spectrometer calculator for DNA and protein concentration.
Stock recipe calculator for tens of commonly used stock solutions.
Units conversion in 14 categories.
Master cocktail mix calculator for multiple reactions.
Clinical: time/date conversion, body-mass index, body area.
MicroHelper: Merge, filter, transform, and normalize microarray data.
Godlist Manager: Batch GenBank search for info or sequence. Generate web links to databases.
Heatmap Viewer: Display high-throughput data using colors. Save image as JPEG file for presentation.
LabLabel: Label and barcode printing
LabInventory: Practical inventory database
PrimerBase: Organize primers.
Searchable by name and sequence.
PeptideBase: Database for peptides.
GradeBook: Grade book for professor/TA
THIS SOFTWARE IS PROVIDED BY CHANG BIOSCIENCE ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL CHANG BIOSCIENCE OR ITS SPONSORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Copyright © 2002-2004 Chang Bioscience, Inc. All rights