Basic Principles and Software for PCR Primer Design -- Physical Principles and Visual-OMP Software for Optimal PCR Design -- OLIGO 7 Primer Analysis Software -- Selection for 3?-End Triplets for Polymerase Chain Reaction Primers -- The Reference Point Method in Primer Design -- PCR Primer Design Using Statistical Modeling -- Developing a Statistical Model for Primer Design -- Genome-Scale PCR Primer Design -- GST-PRIME -- Genome-Scale Probe and Primer Design with PRIMEGENS -- Repeat Masking for PCR Primer Design -- SNPbox -- Fast Masking of Repeated Primer Binding Sites in Eukaryotic Genomes -- Multiplex PCR Primer Design -- Degenerate Primer Design -- An Iterative Method for Selecting Degenerate Multiplex PCR Primers -- Primer Design for Multiplexed Genotyping -- MultiPLX -- MultiPrimer -- Allele-specific PCR -- Modified Oligonucleotides as Tools for Allele-Specific Amplification -- AlleleID -- Long PCR Primer Design -- Designing Primers for Whole Genome PCR Scanning Using the Software Package GenoFrag -- DNA Methylation Mapping -- Designing PCR Primer for DNA Methylation Mapping -- BiSearch -- Graphical Design of Primers with PerlPrimer.

In the past decade, molecular biology has been transformed from the art of cloning a single gene to a statistical science measuring and calculating properties of entire genomes. New high-throughput methods have been developed for genome sequencing and studying the cell at different systematic levels such as transcriptome, proteome, metabolome and other -omes. At the heart of most high-throughput methods is the technique of polymerase chain reaction (PCR). PCR Primer Design focuses on primer design, which is critical to both the efficiency and the accuracy of the PCR. With intricate descriptions of basic approaches as well as specialized methods, this volume is an exceptional reference for all those involved in studying the genome. In PCR Primer Design, authors describe basic approaches for PCR primer design in addition to specialized methods. These state-of-the-art methods can be used for both genome-scale experiments and for small-scale individual PCR amplifications. This volume will be useful for organizations performing whole genome studies, companies designing instruments that utilize PCR, and individual scientists - geneticists, molecular biologists, molecular geneticists, and more - who routinely use PCR in their research.