PCR primer design /

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作者：edited by Anton Yuryev.

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ISBN：9781588297259

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Summary: Publisher Summary 1 Contributors in bioinformatics, molecular genetics, and computer science describe basic and specialized approaches for polymerase chain reaction (PCR) primer design. The methods can be used for both genome-scale experiments and for small-scale individual PCR amplifications. Material is in sections on basic principles and software, genome-scale PCR primer design, multiplex PCR primer design, allele-specific PCR, long PCR primer design, and DNA methylation mapping. The book will be useful as a reference for organizations performing whole genome studies, companies designing instruments that utilize PCR, and individual scientists--geneticists, molecular biologists, and molecular geneticists--who routinely use PCRA in their research. Yuryev is a genomics researcher in the private sector. Annotation 漏2007 Book News, Inc., Portland, OR (booknews.com) Publisher Summary 2 At the heart of most high-throughput methods is the technique of polymerase chain reaction (PCR). This book 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, "PCR Primer Design" is an exceptional reference for all those involved in studying the genome. Publisher Summary 3 At the heart of most high-throughput methods is the technique of polymerase chain reaction (PCR). This book 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, "PCR Primer Design" is an exceptional reference for all those involved in studying the genome.

ART: BASIC PRINCPLEs AND SOFTWARE FOR PCR
PRIMER DESIGN
1 Physical Principles and Visual-OMP Software
for Optimal PCR Design
ohn SantaLucia, fr .................. .......
2 OLIGO 7 Primer Analysis Software
W ojciech Rychlik .................................................
3. Selection for 3'-End Triplets for Po ymerase
Chain Reaction Primers
Kenji Onodera ...................
4. The Reference Point Method in Primer Design
Thomas Ka pke. .5. .. ..... .... . ..... ... ... . .
5 PCR Primer Design Using Statistical Modeling
Anton Yuryev . .............. ........ ... ... 93
6. Developing a Statistical Model for Primer Design
anpi Huang and Aton Yuryev ..... .... ... ...
PART : GENOME -SCALE PC PRIER DESGN
7. GST-PRIME: An Algorithm for Genome-Wide Primer Design
Dario Leister and Claudio Varotto ....... ........ ......
8. Genome-Scale Probe and Primer Design
with PRIMEGENS
Gyan Prakash Srivastava and Dong X ............................159
A.Reeat Masking for PCR Primer Design
9. SNPbox: Web-Based High-Throughput Primer Design
with an Eye for Repetitive Sequences
Stefan eckx, Peter De Rijk, Wi Glassee, Christine Van
Broeckhoven, and urgen Del-Favero ....... ............. 1
i0 Fast Maskiing o Repea ed Primer Binding Sites in Eukaryotic
Reidar Andreson, Lauris Kaplinski and Maido Remm.............. 201
iplx PCR Primer Design
Si. Deenerate Primer Design: Theoetical Analysis and the HYDEN
Program
Chair Linhart and Ron Shamir .... ..... .. .. ................... 221
12. A Ite rtive Method or Selecting Degenerate Multiplex PCR
Primers
Rihard Souvenir, Jeremy Buhler, Gary Stormo, and Weixiong
Zhang ...... .. .... . ... ...... ......... ............... 245
3. Primer Design for Muitiplexed Genotyping
ars K derali ............. . . . . . . . . . ......... ..... 269
4. MuiiPL \X: Automatic Grouping and Evaluation
oi PCR Primers
wris Kaplinski and Maido Remm ........................ ..... 287
15. MuiiPrmer: A System for Microarra P CR
Primer Design
Roban Fernandes and Steven Skiena ............ ..... 30
C Aiele,specftic PCR
SV. Modifie Oiigonucleotides as Tools for Allee-Specific
Amplification
AMichael Strerath, Ilka Detmer, ens Gaster,
and Andreas M arx ...... . .. ...... ...................... .... 317
i7. AdelelD: A Pathogen Detection and Identification ystem
Arun Apte and Siddharth Singh ............. ............ 329
D.Log PCR Primer Design
I . Designing Primers for Whole Genome PCR Scanning
sin. the Software Package GenoFrag: A Software Package
for the Design of Primers Dedicated to Whole-Genome
Scanning by LR-PCR
Nour Ben Zakour and Yves Le oir ..... ......... ............. 349
SDNA Meth[aion Mapping
19. nDsigng PCR Primer for DNA Methvlation Mapping
Liong-Cheng Li. . ....... ........ ...... . . ...... 371
20. BiSearch: ePCR Tool for Native or Bisulfite-Treated Genomic
Template
Tamaas Arinyi and Gabor E. Tusnidy:................... ....... 385
2 Graphical Design of Primers with Per Primer
Owen M arshall .. . ... ... . . . ................... . 403

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