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The PCR Jump Station
The ultimate Web page for information and links on all aspects of the
Polymerase Chain Reaction (PCR).
GeneFisher
GeneFisher processes aligned or unaligned sequences.
GeneFisher comes with a built in alignment tool that feeds the results
directly into the next step. You have the option of looking at a
graphical representation of the alignments and the consensus sequence
that is really useful for a variety of tasks, not just primer design.
At this point you can reject the alignment and adjust the parameters to
try again or you can continue to the primer design step.
GeneWalker
GeneWalker helps you designing your primers. It is a powerful tool, yet
it is based on the philosophy of ease to use. GeneWalker allows you to
work with two primer sequences simultaneously. You can also toggle
between reversed complementary primer sequences. Basic functions
includes calculation of primer secondary structures, primer annealing
properties as well as primer dimers. GeneWalker also helps you to
easily connect to EMBLs databases.
CyberGene
CyberGene is a company that provides commercial oligonucleotide
synthesis, DNA sequencing, genotyping and bioinformatics services. They
also offer this free primer design utility to help you test oligos
before you spend time and money synthesising unsuitable ones.
Web Primer
An application that designs primers for PCR or sequencing purposes. The
user must choose the purpose for which the primers will be used, and
either specify a locus name or enter a sequence.
Primer Design
A free primer design utility, from the EMBL.
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 Primers
Web Primers is a tool for graphically displaying primer sites along a
target sequence. You are presented with an image showing the relative
positions of the selected primers, their direction, and a separate list
of the primers themselves.
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.
NetPrimer
NetPrimer combines the latest primer design algorithms with a web-based
interface allowing the user to analyze primers over the Internet. All
primers are analyzed for melting temperature using the nearest neighbor
thermodynamic theory to ensure accurate Tm prediction. Primers are
analyzed for all secondary structures including hairpins, self-dimers,
and cross-dimers in primer pairs. This ensures the availability of the
primer for the reaction as well as minimizing the formation of primer
dimer. The program eases quantitation of primers by calculating primer
molecular weight and optical activity. To facilitate the selection of
an optimal primer, each primer is given a rating based on the stability
of its secondary structures. A comprehensive analysis report can be
printed for individual primers or primer pairs.
Cassandra - Recognition of protein-coding segments for PCR
Traditionally, the use of gene predictions in experimental practice
amounts to construction of oligonucleotide probes or PCR primers and a
biologist is forced to guess the primer on the top of not very reliable
prediction. CASSANDRA is a program designed for recognition of coding
segments, that is, segments situated within protein-coding DNA regions
of higher eukaryotes, without direct recognition of complete genes. It
produces a list of candidate segments that is virtually guaranteed to
contain a given number of probes or primers situated within exons. The
list of candidate segments is can be optimized by different parameters
that depend on particular experiment that will utilize these segments.
At present the program is optimized for the following two problems:
GenePrimer - Computational support of gene identification experiments
This software implements an algorithm for experimental gene
identification by multiple PCR amplifications.
Since current algorithms for gene recognition make mistakes, biologists have to perform experimental gene identification to eliminate errors in predictions. Conventional approaches amount to `guessing' PCR primers on top of unreliable gene predictions and frequently lead to wasting experimental efforts. An algorithm which eliminates the need of gene verification in some cases is the Las Vegas algorithm for gene recognition. We bypass the unreliable gene prediction step and propose an approach geared towards experimental gene identification. The algorithm locates a set of PCR primers which relatively uniformly cover the exons and can be used for RT-PCR and further sequencing of (unknown) mRNA.
rawprimer - a tool for selection of PCR primers
This page provides an interface to a PCR primer selection program based
on xprimer.
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.
This version of xprimer produces no graphics. It is set up to use human and dog repeat files and several species models. The query sequence (raw sequence with no header - only agct in either case are significant) can be dragged into the textarea in the interface.
Choosing Primers for sequencing
Information provided by the DNA sequencing facility at the University of
Chicago Cancer Research Centre.
Design of Primers for Automated Sequencing
Guide to designing primers from the DNA sequencing core facility at the
University of Michigan.
Any Comments, Questions? Support@hgmp.mrc.ac.uk