The user must choose a purpose for the primers to be designed.
Current choices are limited to sequencing and PCR. Sequencing primers
will be evenly spaced along the DNA. PCR primers will be at the ends
of the DNA selected in a region of DNA, the length of which is user defined.
The user must the DNA sequence from which the
primers will be chosen. The DNA
sequence may include numbers but should NOT include letter characters
(other than the DNA sequence).
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 influenced by the user and are further described below.
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, for which
strand(s) to order primers, the approximate distance between primers,
the length and percent GC content of the primers, and the maximum self-annealing of the primers.