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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.
PCR primer design. Contents
Part I. Basic Principles and software for PCR primer design
Chapter 1. Physical Principles and Visual-OMP Software for Optimal PCR
Chapter 2. Oligo 7 Primer Analysis Software
Chapter 3. Selection for 3' end triplets for polymerase chain reaction primers
Chapter 4. The reference point method in primer design
Chapter 5. PCR primer design using statistical modeling
Chapter 6. Developing a Statistical Model for Primer Design
Part II. Genome scale PCR primer design
Chapter 7. GST-PRIME: An Algorithm for Genome-Wide Primer Design
Chapter 8. Genome-Scale Probe and Primer Design with PRIMEGENS
Repeat masking for PCR primer design
Chapter 9. SNPbox: web-based high-throughput primer design with an eye for repetitive sequences.
Chapter 10. Fast masking of repeated primer binding sites in eukaryotic genomes
Multiplex PCR primer design
Chapter 11. Degenerate Primer Design: Theoretical Analysis and the
Chapter 12. An Iterative Method for Selecting Degenerate Multiplex PCR
Chapter 13. Primer-design for multiplexed genotyping
Chapter 14. MultiPLX: automatic grouping and evaluation of PCR primers
Chapter 15. MultiPrimer: A system for Microarray PCR Primer Design
Chapter 16. Modified oligonucleotides as tools for allele-specific amplification
Chapter 17. AlleleID: A Pathogen Detection and Identification System
Long PCR primer design
Chapter 18. GenoFrag, a software package for the design of primers dedicated to whole genome scanning by LR-PCR.
DNA methylation mapping
Chapter 19. Designing PCR primer for DNA methylation mapping
Chapter 20. BiSearch: ePCR tool for native or bisulfite treated genomic template.
Chapter 21. Graphical design of primers with PerlPrimer