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publication info
A. Yuryev, Humana Press, 2007, 431 pp., hard cover
General description
In this book 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 perfomring whole genome studies, companies designing instruments that utilize PCR, and individual scientists who routinely use PCR in their research.
Table of Contents
PART I: BASIC PRINCIPLES AND SOFTWARE FOR PCR PRIMER DESIGN
1. Physical Principles and visual -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
SECTION A: REPEAT MASKING FOR PCR PRIMER DESIGNS
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
SECTION B: MULTIPLEX PCR PRIMER DESIGN
11. Degenerate primer design: Theoretical analysis and the HYDEN program
12. An iterative method for selecting degenerate multilex PCR primers
13. Primer design for multiplexed genotyping
14. MultiPLEX: Automatic grouping and evaluation of PCR primers
15. Multiprimer: a system for microarry PCR primer design
SECTION C: ALLELE SPECIFIC PCR
16. Modified Oligonucleotides as tools for allele specific amplification
17. AlleleID: A pathogen detection and identification system
SECTION D: LONG PCR PRIMER DESIGN
18. Designing primers for whole genome PCR scanning using the software packagin GenoFrag: a software package for the design of primers dedicated to whole genome scanning by LR-PCR
SECTION 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 PerlPrimer
Index
1. Physical Principles and visual -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
SECTION A: REPEAT MASKING FOR PCR PRIMER DESIGNS
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
SECTION B: MULTIPLEX PCR PRIMER DESIGN
11. Degenerate primer design: Theoretical analysis and the HYDEN program
12. An iterative method for selecting degenerate multilex PCR primers
13. Primer design for multiplexed genotyping
14. MultiPLEX: Automatic grouping and evaluation of PCR primers
15. Multiprimer: a system for microarry PCR primer design
SECTION C: ALLELE SPECIFIC PCR
16. Modified Oligonucleotides as tools for allele specific amplification
17. AlleleID: A pathogen detection and identification system
SECTION D: LONG PCR PRIMER DESIGN
18. Designing primers for whole genome PCR scanning using the software packagin GenoFrag: a software package for the design of primers dedicated to whole genome scanning by LR-PCR
SECTION 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 PerlPrimer
Index
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