Using Web Primer
Uses & Input
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.
DNA Source
The user must also enter either a locus name or an actual DNA
sequence; either will then act as the source of DNA from which the
primers are chosen. For the Locus field, any standard ORF
name (i.e. YBL004W) and many gene names (i.e. BUD4, TUB2) are
allowed. If an entry in this field is ambiguous (matching more than
one entry in the database) a list of matching entries is created and
the user is requested to choose one. An example of this is YJL12 which
matches ORFs YJL120W through YJL129C. If these ORFs have gene names
associated with them this name is present as well
(i.e. YJL125C=GCD14). Entries which match MORE than 25 ORFs will not
be processed and the user is requested to refine the entry. 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 influence by the user and are further described below.
Sequencing Primers
[more]
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.
Return to Saccharomyces Genome Database