PCR primer design / edited by Anton Yuryev. — Totowa : Humana Press, c2007. – (58.17/M592/v.402)

Contents

        Contents
    
    Preface v
    Contributors xi
    PART I: BASIC PRINCIPLES AND SOFTWARE FOR PCR PRIMER DESIGN
     1. Physical Principles and VisuaI-OMP Software for Optimal PCR Design
     2. OLIGO 7 Primer Analysis Software
     3. Selection for 3'-End Triplets for Polymerase Chain Reaction Primers
     4. The Reference Point Method in Primer Design
     5. PCR Primer Design Using Statistical Modeling
     6. Developing a Statistical Model for Primer Design
    PART II: GENOME-SCALE PCR PRIMER DESIGN
     7. GST-PRIME: An Algorithm for Genome-Wide Primer Design
     8. Genome-Scale Probe and Primer Design with PRIMEGENS
    A. Repeat Masking for PCR Primer Design
     9. SNPbox: Web-Based High-Throughput Primer Design with an Eye for Repetitive Sequences
     10. Fast Masking of Repeated Primer Binding Sites in Eukaryotic Genomes
    B. Multiplex PCR Primer Design
     11. Degenerate Primer Design: Theoretical Analysis and the HYDEN Program
     12. An Iterative Method for Selecting Degenerate Multiplex PCR Primers
     13. Primer Design for Multiplexed Genotyping
     14. MultiPLX: Automatic Grouping and Evaluation of PCR Primers
     15. MultiPrimer: A System for Microarray PCR Primer Design
    C. Allele-specific PCR
     16. Modified Oligonucleotides as Tools for Allele-Specific Amplification
     17. AlleleID: A Pathogen Detection and Identification System
    D. Long PCR Primer Design
     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
     19. Designing PCR Primer for DNA Methylation Mapping
     20. BiSearch: ePCR Tool for Native or Bisulfite-Treated Genomic Template
     21. Graphical Design of Primers with PerIPrimer
    Index 415