Primo HighLow 1.3: For High/Low-GC and Repeats
| Primo HighLow 1.3 is our first
attempt in improving PCR primer design for PCR templates with high or low-GC
content or repeats, and long templates. Please bear with us if it didn't improve
your PCR. If you have tried it, please
send us a message
no matter whether it has helped you or not. Your feedback will allow us to improve the
software and will be greatly appreciated.
Primo HighLow attempts to find better PCR primers by selecting primers that have few chances
of annealing internally. For a schematic illustration of the principle, see the figure at
the left-bottom of this page.
For typical templates, please use Primo Pro.
Order Primo Pro
New: batch mode. See also
|| Warning! Uncheck "Avoid background priming" if PCR template is not human cDNA. Read
user manuel for details. |
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.
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
Compare Primo to other online primer design software and find
Primo HighLow 1.3
Primo HighLow hypothesizes that the best PCR primers for a template with high or
low GC contents are primers that can initiate amplification only at the desired
positions. Primers whose 3' sequences match the internal sequences on the
template may accidentally initiate amplification. Once initiated the
internal sequences will be amplified with better efficiency because they are
shorter than the full-length product. For templates that are GC or AT-rich,
have repeats, or are long, some primers may have 3' sequences that will match
internally at a high frequency, thus make it difficult to amplify the full-length
product. By eliminating those primers, we hope to select primers that will have
a better chance of amplifying the full-length product.
Figure 1. Red primers do not pair internally, thus may have higher amplification
efficiency for the full-length product. Other primers (marked with x) may pair
internally in either sense or antisense directions. The internal pairing may
contribute to amplification noises.
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
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