Automated DNA Sequencing and Analysis

Content: 
Front Matter, Page iii
Copyright, Page iv
Preface, Pages v-vi, M.D. ADAMS, C. FIELDS, J. CRAIG VENTER
Acknowledgements, Page vii
CHAPTER ONE - The Efficiency of Automated DNA Sequencing, Pages 3-10, E.Y. CHEN
CHAPTER TWO - Automated Multiplex Sequencing, Pages 11-16, G.M. CHURCH, G. GRYAN, N. LAKEY, S. KIEFFER-HIGGINS, L. MINTZ, S. KIEFFER-HIGGINS, M. TEMPLE, L. JAEHN, H. GHAZIZADEH, K. ROBISON, M. RUBENFIELD, P. RICHTERICH
CHAPTER THREE - Application of Capillary Array Electrophoresis to DNA Sequencing, Pages 17-28, X.C. HUANG, R.A. MATHIES
CHAPTER FOUR - Sequencing by Hybridization, Pages 29-36, R. DRMANAC, S. DRMANAC, J. JARVIS, I. LABAT
CHAPTER FIVE - Shotgun Sequencing, Pages 37-41, A. MARTIN-GALLARDO, J. LAMERDIN, A. CARRANO
CHAPTER SIX - Shotgun Cloning as the Strategy of Choice to Generate Templates for High-throughput Dideoxynucleotide Sequencing, Pages 42-50, A. BODENTEICH, S. CHISSOE, Y.-F. WANG, B.A. ROE
CHAPTER SEVEN - Transposon-facilitated Large-scale DNA Sequencing, Pages 51-59, C.M. BERG, G. WANG, K. ISONO, H. KASAI, D.E. BERG
CHAPTER EIGHT - Transposon-facilitated Sequencing: an Effective Set of Procedures to Sequence DNA Fragments Smaller than 4 kb, Pages 60-64, C.H. MARTIN, C.A. MAYEDA, C.A. DAVIS, M.P. STRATHMANN, M.J. PALAZZOLO
CHAPTER NINE - Construction of Exonuclease III Generated Nested Deletion Sets for Rapid DNA Sequencing, Pages 65-70, L.-I. LIU, R.D. FLEISCHMANN
CHAPTER TEN - Expressed Sequence Tags as Tools for Physiology and Genomics, Pages 71-76, M.D. ADAMS
CHAPTER ELEVEN - The Use of Automated DNA Sequencing in the Analysis of cDNAs of Model Organisms, Pages 77-80, W.R. McCOMBIE
CHAPTER TWELVE - Applications of Cosmid Libraries in Genome Mapping and Sequencing Efforts, Pages 83-88, R.L. STALLINGS, N.A. DOGGETT, A. FORD, J. LONGMIRE, C.E. HILDEBRAND, L.L. DEAVEN, R.K. MOYZIS
CHAPTER THIRTEEN - A Role for the P1 Cloning System in Genome Analysis, Pages 89-95, D.A. SMOLLER, W.J. KIMMERLY, O. HUBBARD, C. ERICSSON, C.H. MARTIN, M.J. PALAZZOLO
CHAPTER FOURTEEN - Generation and Mapping of Chromosome Specific Sequence-tagged Sites, Pages 96-101, N.A. DOGGETT, D.L. GRADY, J.L. LONGMIRE, L.L. DEAVEN
CHAPTER FIFTEEN - Construction of cDNA Libraries, Pages 102-109, R.F. MORENO-PALANQUES, R.A. FULDNER
CHAPTER SIXTEEN - Construction of Directionally Cloned cDNA Libraries in Phagemid Vectors, Pages 110-114, M.B. SOARES
CHAPTER SEVENTEEN - Construction of Directional cDNA Libraries, Pages 115-119, A. SWAROOP
CHAPTER EIGHTEEN - Generation of Expressed Sequence Tags of Brassica napus by Single-run Partial Sequencing of Random cDNA Clones, Pages 120-122, J.M. KWAK, H.G. NAM
CHAPTER NINETEEN - Abundance Screening of Human cDNA Libraries, Pages 123-125, J.M. SIKELA, T.J. STEVENS, J.A. HOPKINS, A.S. WILCOX, J. GLOD, A.S. KHAN, A.K. ORPANA
CHAPTER TWENTY - High Density Grid Technologies, Pages 126-130, G. LENNON
CHAPTER TWENTY-ONE - Solid Phase Preparation of Sequencing Templates from PCR Products, Pages 133-138, D.R. SIBSON
CHAPTER TWENTY-TWO - Automatic Preparation of DNA Templates for Sequencing on the ABI Catalyst Robotic Workstation, Pages 139-145, A. HOLMBERG, G. FRY, M. UHLÉAN
CHAPTER TWENTY-THREE - Custom Magnetic Particles: Their Use in DNA Purification, Pages 146-155, T. HAWKINS
CHAPTER TWENTY-FOUR - Large-scale, Automated Sequencing of Human Chromosomal Regions, Pages 159-166, W.R. McCOMBIE, A. MARTIN-GALLARDO
CHAPTER TWENTY-FIVE - Zen and the Art of Large-scale Genomic Sequencing, Pages 167-174, L. ROWEN, B.F. KOOP
CHAPTER TWENTY-SIX - Automated Dye-Terminator DNA Sequencing, Pages 175-181, J.M. KELLEY
CHAPTER TWENTY-SEVEN - PCR Based Strategies for Gap Closure in Large-scale Sequencing Projects, Pages 182-190, D.M. MUZNY, S. RICHARDS, Y. SHEN, R.A. GIBBS
CHAPTER TWENTY-EIGHT - Sequence Map Gaps and Directed Reverse Sequencing for the Completion of Large Sequencing Projects, Pages 191-198, S. RICHARDS, D.M. MUZNY, A.B. CIVITELLO, F. LU, R.A. GIBBS
CHAPTER TWENTY-NINE - Optimized Methods for Large-scale Shotgun DNA Sequencing in Alu-rich Genomic Regions, Pages 199-210, F.J.M. IRIS
CHAPTER THIRTY - Use of Dimethyl Sulfoxide to Improve Fluorescent, Taq Cycle Sequencing, Pages 211-215, S.G. BURGETT, P.R. ROSTECK JR
CHAPTER THIRTY-ONE - Neural Networks for Automated Base-calling of Gel-based DNA Sequencing Ladders, Pages 219-230, C. TIBBETTS, J.M. BOWLING, J.B. GOLDEN III
CHAPTER THIRTY-TWO - Advances in Sequence Assembly, Pages 231-248, E.W. MYERS
CHAPTER THIRTY-THREE - Computer-aided Sequence Reconstruction: Software Support for Multiple Largescale Sequencing Strategies, Pages 239-248, S. HONDA, N.W. PARROTT, C.B. LAWRENCE
CHAPTER THIRTY-FOUR - Stochastic Optimization Tools for Genomic Sequence Assembly, Pages 249-259, C. BURKS, M.L. ENGLE, S. FORREST, R.J. PARSONS, C.A. SODERLUND, P.E. STOLORZ
CHAPTER THIRTY-FIVE - Software Tools for Protein Similarity Searching, Pages 263-274, G. SUTTON, A.R. KERLAVAGE
CHAPTER THIRTY-SIX - Large-scale Sequence Analysis, Pages 267-271, J.-M. CLAVERIE
CHAPTER THIRTY-SEVEN - Finding Frameshift Errors in Anonymous DNA, Pages 280-288, J.W. SHAVLIK
CHAPTER THIRTY-EIGHT - Software Tools For Primer Site Prediction and Sequence Similarity Searches, Pages 289-293, B. RAPPAPORT, J. GATEWOOD, C. FIELDS, N. DOGGETT
CHAPTER THIRTY-NINE - Approaches to Identification and Analysis of Interspersed Repetitive DNA Sequences, Pages 294-296, J. JURKA
CHAPTER FORTY - Computational Tools for DNA Sequence Analysis, Pages 299-308, O. WHITE, T. DUNNING
CHAPTER FORTY-ONE - A Practical Guide to the GRAIL E-mail Server, Pages 307-312, E.C. UBERBACHER, X. GUAN, R.J. MURAL
CHAPTER FORTY-TWO - Searching for Homologies to Protein Blocks by Electronic Mail, Pages 313-320, S. HENIKOFF, J.G. HENIKOFF, S. AGUS, J.C. WALLACE
CHAPTER FORTY-THREE - Integrating Computational and Experimental Methods for Gene Discovery, Pages 321-325, C. FIELDS
CHAPTER FORTY-FOUR - Design Issues in Developing Laboratory Information Management Systems, Pages 329-341, S. LEWIS
FORTY-FIVE - Construction of Directionally Cloned cDNA Libraries in Phagemid Vectors, Pages 339-344, M.B. SOARES
CHAPTER FORTY-SIX - ACEDB: A Tool for Biological Information, Pages 347-356, J.M. CHERRY, S.W. CARTINHOUR
CHAPTER FORTY-SEVEN - The Integration of Curated Biological Databases, Pages 357-361, R. OVERBEEK, M. PRICE
Appendix - Sources of Sequence Analysis Software, Page 362
Index, Pages 363-368