Contents
Preface v
Contents of the Companion Volume xi
Contributors xi
1 BAC Library Construction
Kazutoyo Osoegawa and Pieter J. de Jong xx
2 Construction of Small Genome BAC Library for Functional
and Genomic Applications
David Smajs, Steven J. Norris, and George M. Weinstock xx
3 Preparation of BAC Libraries from Bacterial Genomes by In Vitro Packaging
Sangita Pal, Solida Mak, and George M. Weinstock xxx
4 Exploring TAR Cloning for Selective Isolation of Genomic Regions
Natalay Kouprina, Vladimir N. Noskov, Maxim Koriabine,
Sun-Hee Leem, and Vladimir Larionov xxx
5 BAC DNA Purification
Tim Svenstrup Poulsen xxx
6 Hybridization-Based Selection of BAC Clones
Chang-Su Lim and Ung-Jin Kim xxx
7 Applications of Interspersed Repeat Sequence (IRS)-PCR
Heike Zimdahl, Claudia GÜsele, Thomas Kreitler, and Margit Knoblauch xxx
8 BAC Mapping by Using Fluorescence In Situ Hybridization
Xiao-Ning Chen and Julie R. Korenberg xxx
9 High Throughput BAC Fingerprinting
Jacqueline Schein, Tamara Kucaba, Mandeep Sekhon, Duane Smailus, Robert Waterston, and Marco Marra xxx
10 BAC End Sequencing
Time Svenstrup Poulsen and Hans Erik Johnsen xxx
11 Radiation Hybrid Mapping with BAC Ends
Michael Olivier, Shannon Brady, and David R. Cox xxx
12 Shotgun Library Construction for DNA Sequencing
Bruce A. Roe xxx
13 Rolling Circle Amplification for Sequencing Templates
Paul F. Predki, Chris Elkin, Hitesh Kapur, Jamie Jett, Susan Lucas, Tijana Glavina, and Trevor Hawkins xxx
14 Transposon-Mediated Sequencing
Rachel Dickhoff and Anup Madan xxx
15 Pyrosequencing: A Tool for DNA Sequencing Analysis
Elahe Elahi and Mostafa Ronaghi xxx
16 The Use of Fimers to Eliminate PCR, Primer-Dimer Artifacts
and to Increase the Yield in BAC Sequencing Reactions
Andrei Malykh, Nikolai Polushin, Alexei Slesarev,
and Sergei Kozyavkin xxx
17 Retrofitting BACs and PACs with LoxP Transposons
to Generate Nested Deletions
Pradeep K. Chatterjee xxx
18 Preparing Nested-Deletion Template DNA for FIGE Analyses
and Position-Specific End Sequencing with Transposon Primers
Pradeep K. Chatterjee and Joseph C. Baker, Jr. xxx
19 BAC Finishing Strategies
Christine Bird and Darren Grafham xxx
20 Using the TIGR Assembler in Shotgun Sequencing Projects
Mihai Pop and Dan Kosack xxx
21 Finishing "Working Draft" BAC Projects by Directed Sequencing
with ThermoFidelase and Fimers
Andrei Malykh, Olga Malykh, Nikolai Polushin, Sergei Kozyavkin, and Alexei Slesarev xxx
22 Optimized Multiplex PCR: An Effective Method for Rapid Gap Closure
Diana Radune and HervÄ Tettelin xxx
23 Assembly of DNA Sequencing Data
Jeremy Schmutz, Jane Grimwood, and Richard M. Myers xxx
24 Sequence Finishing
Jeremy Schmutz, Jane Grimwood, and Richard M. Myers xxx
25 Quality Assessment of Finished BAC Sequences
Jeremy Schmutz, Jane Grimwood, and Richard M Myers xxx
Index xxx
CONTENTS OF THE COMPANION VOLUME
Volume 1: Library Construction, Physical Mapping, and Sequencing
1 BAC Library Construction
Kazutoyo Osoegawa and Pieter J. de Jong
2 Construction of Small Genome BAC Library for Functional
and Genomic Applications
David Smajs, Steven J. Norris, and George M. Weinstock
3 Preparation of BAC Libraries from Bacterial Genomes by In Vitro Packaging
Sangita Pal, Solida Mak, and George M. Weinstock
4 Exploring TAR Cloning for Selective Isolation of Genomic Regions
Natalay Kouprina, Vladimir N. Noskov, Maxim Koriabine,
Sun-Hee Leem, and Vladimir Larionov
5 BAC DNA Purification
Tim Svenstrup Poulsen
6 Hybridization-Based Selection of BAC Clones
Chang-Su Lim and Ung-Jin Kim
7 Applications of Interspersed Repeat Sequence (IRS)-PCR
Heike Zimdahl, Claudia GÜsele, Thomas Kreitler, and Margit Knoblauch
8 BAC Mapping by Using Fluorescence In Situ Hybridization
Xiao-Ning Chen and Julie R. Korenberg
9 High Throughput BAC Fingerprinting
Jacqueline Schein, Tamara Kucaba, Mandeep Sekhon, Duane Smailus, Robert Waterston, and Marco Marra
10 BAC End Sequencing
Time Svenstrup Poulsen and Hans Erik Johnsen
11 Radiation Hybrid Mapping with BAC Ends
Michael Olivier, Shannon Brady, and David R. Cox
12 Shotgun Library Construction for DNA Sequencing
Bruce A. Roe
13 Rolling Circle Amplification for Sequencing Templates
Paul F. Predki, Chris Elkin, Hitesh Kapur, Jamie Jett, Susan Lucas, Tijana Glavina, and Trevor Hawkins
14 Transposon-Mediated Sequencing
Rachel Dickhoff and Anup Madan
15 Pyrosequencing: A Tool for DNA Sequencing Analysis
Elahe Elahi and Mostafa Ronaghi
16 The Use of Fimers to Eliminate PCR, Primer-Dimer Artifacts
and to Increase the Yield in BAC Sequencing Reactions
Andrei Malykh, Nikolai Polushin, Alexei Slesarev,
and Sergei Kozyavkin
17 Retrofitting BACs and PACs with LoxP Transposons
to Generate Nested Deletions
Pradeep K. Chatterjee
18 Preparing Nested-Deletion Template DNA for FIGE Analyses
and Position-Specific End Sequencing with Transposon Primers
Pradeep K. Chatterjee and Joseph C. Baker, Jr.
19 BAC Finishing Strategies
Christine Bird and Darren Grafham
20 Using the TIGR Assembler in Shotgun Sequencing Projects
Mihai Pop and Dan Kosack
21 Finishing "Working Draft" BAC Projects by Directed Sequencing
with ThermoFidelase and Fimers
Andrei Malykh, Olga Malykh, Nikolai Polushin, Sergei Kozyavkin, and Alexei Slesarev
22 Optimized Multiplex PCR: An Effective Method for Rapid Gap Closure
Diana Radune and HervÄ Tettelin
23 Assembly of DNA Sequencing Data
Jeremy Schmutz, Jane Grimwood, and Richard M. Myers
24 Sequence Finishing
Jeremy Schmutz, Jane Grimwood, and Richard M. Myers
25 Quality Assessment of Finished BAC Sequences
Jeremy Schmutz, Jane Grimwood, and Richard M Myers
CONTENTS OF THE COMPANION VOLUME
Volume 2: Functional Studies
1 Use of BAC End Sequences for SNP Discovery
Michael M. Weil, Rashmi Pershad, Ruoping Wang,
and Sheng Zhao
2 Exon Trapping for Positional Cloning and Fingerprinting
Scott E. Wenderfer and John J. Monaco
3 Isolation of CpG Islands from BAC Clones
Using a Methyl-CpG Binding Column
Sally H. Cross
4 BAC Microarray-Based Comparative Genomic Hybridization
Antoine M. Snijders, Richard Segraves,
Stephanie Blackwood, Daniel Pinkel,
and Donna G. Albertson
5 Large DNA Transformation in Plants
Sangdun Choi
6 Retrofitting BACs with a Selectable Marker for Transfection
Zunde Wang, Angelika Longacre, and Peter Engler
7 BAC Modification Using a RecA Expressing
Shuttle Vector System
Nathan Mise and Philip Avner
8 Bacterial Artificial Chromosome Engineering
Srividya Swaminathan and Shyam K. Sharan
9 ET Recombination: DNA Engineering Using Homologous
Recombination in E. coli
Joep P. P. Muyrers, Youming Zhang, Vladmir Benes,
Giuseppe Testa, Jeanette M. J. Rientjes,
and A. Francis Stewart
10 BAC Engineering for the Generation of ES Cell Targeting
Constructs and Mouse Transgenes
A. Francis Stewart
11 Microinjection of BAC DNA into the Pronuclei
of Fertilized Mouse Oocytes
Kristina Vintersten, Giuseppe Testa, and A. Francis Stewart
12 Generation of BAC Transgenic Mice
Vikki M. Marshall, Jan Allison, Tanya Templeton,
and Simon J. Foote
13 BAC Rescue: A Tool for Functional Analysis of the Mouse Genome
Deborah A. Swing and Shyam K. Sharan
14 Herpesviruses: A Brief Overview
Mathias Ackermann
15 Cloning of _-Herpesvirus Genomes
as Bacterial Artificial Chromosomes
Eva-Maria Borst, Irena Crnkovic-Mertens,
and Martin Messerle
16 Construction of HSV-1 BACs and Their Use for Packaging
of HSV-1 Based Amplicon Vectors
Thomas G. H. Heister, A. VÜgtlin, Lars Mller, Irma Heid,
and Cornel Fraefel
17 Mutagenesis of Viral BACs with Linear PCR Fragments
(ET Recombination)
Markus Wagner and Ulrich H. Koszinowski
18 Mutagenesis of Herpesvirus BAC Plasmids
by Allele Replacement
Eva Maria Borst, GyÜrgy Pùsfai, Frank Pogoda,
and Martin Messerle
19 Herpesvirus Genome Mutagenesis
by Transposon-Mediated Strategies
Alistair McGregor and Mark R. Schleiss
20 Protective DNA Vaccination by Particle Bombardment
Using BAC DNA Containing a Replication-Competent,
Packaging-Defective Genome of Herpes Simplex Virus Type I
Mark Suter and Hans Peter Hefti