PCR primer design/ edited by Anton Yuryev.

Part I. Basic Principles and software for PCR primer design
Chapter 1. Physical Principles and Visual-OMP Software for Optimal PCRDesign
Chapter 2. OLIGO 7 Primer Analysis Software
Chapter 3. Selection for 3'-End Triplets for Polymerase chain reactionprimers
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
A. Repeat masking for PCR primer design
Chapter 9. SNPbox: web-based high-throughput primer design with an eyefor repetitive sequences
Chapter 10. Fast masking of repeated primer binding sites in eukaryotic genomes
B. Multiplex PCR primer design
Chapter 11. Degenerate Primer Design: Theoretical Analysis and the HYDEN program
Chapter 12. An Iterative Method for Selecting Degenerate Multiplex PCR Primers
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
C. Allele-specific PCR
Chapter 16. Modified oligonucleotides as tools for allele-specific amplification
Chapter 17. AlleleID: A Pathogen Detection and Identification System
D. Long PCR primer design
Chapter 18. Designing Primers for whole Genome PCR scanning using the software package GenoFrag: a software package for the design of primers dedicated to whole genome scanning by LR-PCR
E. DNA methylation mapping
Chapter 19. Designing PCR primer for DNA methylation mapping
Chapter 20. BiSearch: ePCR tool for native or bisulfite treated genomictemplate
Chapter 21. Graphical design of primers with PerlPrimer