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Welcome to the GenomeWeb Primer Design Search for:

The PCR Jump Station
Primer3
Web Primer
xprimer
POLAND - melting profiles of double stranded DNA
CODEHOP - PCR primers designed from protein multiple sequence alignments
Williamstone Enterprises Primer Design

Detailed information on the above options

The PCR Jump Station
The ultimate Web page for information and links on all aspects of the Polymerase Chain Reaction (PCR).

Primer3
Primer3 picks primers for PCR reactions, according to the conditions specified by the user. Primer considers things like melting temperature, concentrations of various solutions in PCR reactions, primer bending and folding, and many other conditions when attempting to choose the optimal pair of primers for a reaction. All of these conditions are user-specifiable, and can vary from reaction to reaction.

Web Primer
PCR primers

There are many factors which influence the success of a pair of primers. Some of the properties of primers which can affect the outcome of PCR include: the GC / AT ratio, length, melting temperature, and the extent of annealing between primers. The location of a primer also heavily influences its usefulness. All of these variables are able to be influence by the user.

Sequencing Primers

Sequencing primers are also highly customizable. Potential valid primers are evenly spaced along the DNA of interest starting at each 5' end. The user is allowed to specify the area of DNA to be sequenced, how many strands to order sequencing primers for, which strand to order primers for, the approximate distance between primers, the length and percent GC content of the primers, and the maximum self annealing of the primers.

xprimer
xprimer is a tool under developement for selection of PCR primers. It is designed for selection of sets of primers along very large queries, all with a relatively narrow Tm range. It is also useful in more traditional PCR applications.

POLAND - melting profiles of double stranded DNA
The Poland server will calculate the thermal denaturation profile of double stranded RNA or DNA based on sequence input and parameter settings in this form. Calculation is based on D. Poland's algorithm in the implementation described by G. Steger.

Calculations can be done for oligonucleotides (>15 bases) or long double strands (>50 bases), respectively.

CODEHOP - PCR primers designed from protein multiple sequence alignments
The CODEHOP program designs PCR (Polymerase Chain Reaction) primers from protein multiple-sequence alignments. The program is intended for cases where the protein sequences are distant from each other and degenerate primers are needed.

The multiple-sequence alignments should be of amino acid sequences of the proteins and be in the Blocks Database format Proper alignments can be obtained by different methods.

The result of the CODEHOP program are suggested degenerate sequences of DNA primers that you can use for PCR. You have to choose appropriate primer pairs, get them synthesized and perform the PCR.

Williamstone Enterprises Primer Design
Provide online DNA oligonucleotide design for free. Links to several oligo manufacturing companies are provided.

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