Automated DNA Sequencing and Analysis

A timely book for DNA researchers, Automated DNA Sequencing and Analysis reviews and assesses the state of the art of automated DNA sequence analysis-from the construction of clone libraries to the developmentof laboratory and community databases. It presents the methodologies and strategies of automated DNA sequence analysis in a way that allows them to be compared and contrasted. By taking a broad view of the process of automated sequence analysis, the present volume bridges the gap between the protocols supplied with instrument and reaction kits and the finalized data presented in the research literature. It will be an invaluable aid to both small laboratories that are interested in taking maximum advantageof automated sequence resources and to groups pursuing large-scale cDNA and genomic sequencing projects.

The field of automation in DAN sequencing and analysis is rapidly moving, this book fulfils those needs, reviews the history of the art and provides pointers to future development.

Sequencing Instruments and Strategies:
E. Chen, The Efficiency of Automated DNA Sequencing.
G.M. Church, G. Gryan, N. Lakey, S. Kieffer-Higgins, L. Mintz, M. Temple, M. Rubenfield, L. Jaehn, H. Ghazizadel, K. Robison, and P. Richterick, Automated Multiplex Sequencing.
X.C. Huang and R.A. Mathies, Application of Capillary Array Electrophoresis to DNA Sequencing.
R. Drmanac, S. Drmanac, J. Jarvis, and I. Labat, Sequencing by Hybridization.
A. Martin-Gallardo, J. Lamerdin, and A. Carrano, Shotgun Sequencing.
A. Bodenteich, S. Chissoe, Y.-F. Wang, and B. Roe, Shotgun Cloning as the Strategy of Choice to Generate Templates for High Throughput Dideoxynucleotide Sequencing.
C.M. Berg, G. Wang, K. Isono, H. Kasai, and D.E. Berg, Transposon-Facilitated Large-Scale DNA Sequencing.
C.H. Martin, C.A. Mayeda, C.A. Davis, M.P. Strathmann, and M. Palazzolo, Transposon-Facilitated Sequencing: An Effective Set of Procedures to Sequence DNA Fragments Smaller than 4kb.
L. Liu and R.D. Fleischmann, Construction of Exonuclease III Nested Deletion Sets for Rapid DNA Sequencing.
M. Adams, Expressed Sequence Tags as Tools for Physiology and Genomics.
W.R. McCombie, The Use of Automated DNA Sequencing in the Analysis of cDNAs of Model Organisms.
Sample Preparation and Sequencing Methods: Libraries:
R.L. Stalligs, N.A. Doggett, A. Ford, J. Longmire, C.E. Hildebrand, L.L. Deaven, and R. Moyzis, Applications of Cosmid Libraries in Genome Mapping and Sequencing Efforts.
D.A. Smoller, W.J. Kimmerly, O. Hubbard, C. Ericsson, C.H. Martin, and M.J. Palazzolo, A Role for the P1 Cloning System in Genome Analysis.
N.A. Doggett, D.L. Grady, J.L. Longmire, and L.L. Deaven, Generation and Mapping of Chromosome Specific Sequence-Tagged Sites (STS).
R. Moreno and R. Fuldner, Construction of cDNA Libraries.
M.B. Soares, Construction of Directionally Cloned cDNA Libraries and Phagemid Vectors.
A. Swaroop, Construction of Directional cDNA Libraries.
J.M. Kwak and J.G. Nam, Preparation of cDNA Libraries from Brassica.
J.M. Sikela, T.J. Stevens, J.A. Hopkins, A.S. Wilcox, J. Glod, A.S. Khan, and A.K. Orpana, Abundance Screening of Human cDNA Libraries.
G. Lennon, High Density Grid Technologies.
Automated Sample Preparation:
D.R. Sibson, Solid Phrase Preparation of Sequencing Templates from PCR Products.
A. Holmberg, G. Fry, and M. Uhlon, Automatic Preparation of DNA Templatesfor Sequencing on the ABI Catalyst Robotic Workstation.
T. Hawkins, Custom Magnetic Particles: Their Use in DNA Purification.
Sequencing Methods:
W.R. McCombie and A. Martin-Gallardo, Large-Scale Automated Sequencing of Human Chromosomal Regions.
L. Rowen and B.F. Koop, Zen and the Art of Large-Scale Genomic Sequencing.
J.M. Kelley, Automated Dye Terminator DNA Sequencing.
D.M. Muzny, S. Richards, Y. Shen, and R.A. Gibbs, PCR Based Strategies for Gap Closure in Large Scale Sequencing Projects.
S. Richards, D.M. Muzny, A.B. Civitello, F. Lu, and R.A. Gibbs, Sequence Map Gaps and Directed Reverse Sequencing for the Completion of Large Sequencing Projects.
F. Iris, Optimized Methods for Large-Scale Shotgun DNASequencing in Alu-Rich Genomic Regions.
S.G. Burgett and P.R. Rosteck, Jr., Use of Dimethylsulfoxide to Improve Fluorescent, Tag Cycle Sequencing.
Informatics: Sequence Assembly Theory and Algorithms:
C. Tibbetts, J.M. Bowling, and J.B. Golden, III, Neural Networks for Automated Base Calling of Gel Based DNA Sequencing Ladders.
G. Myers, Advances in Sequence Assembly.
S. Honda, N.W. Parrott, and C.B. Lawrence, Computer Aided Sequence Reconstruction: Software Support for Multiple Large-Scale Sequencing Strategies.
C. Burks, M.L. Engle, S. Forrest, R.J. Parsons, C.A. Soderlund, and P.E. Stolorz, Relaxation and Optimization Methods for Sequence Assembly.
Data Analysis Tools:
G. Sutton and T. Kerlavage, Software Tools for Protein Similarity Searching.
J.M. Claverie, Large-Scale Sequence Analysis.
J. Shavlik, Finding Frame Shift Errors in Anonymous DNA.
B. Rappaport, J. Gatewood, C. Fields, and N. Doggett, Integrating Repeat Identification withThermal Calculations.
J. Jurka, Approaches to Identification and Analysis of Interspersed Repetitive DNA Sequences.
O. White and T. Dunning, Compositional Properties of Exons and Introns.
E.C. Uberbacher, X. Guan, and R.J. Mural, A Practical Guide to the GRAIL Email Server.
S. Henikoff, J. Henikoff, S. Agus, and J.C. Wallace, Searching for Homologies to Protein Blocks by Electronic Mail.
C. Fields, Integrating Computational and Experimental Methods.
Data Management and Databases:
S. Lewis, Design Issues in Developing Laboratory Information Management Systems.
J. Cuticchia, A Relational Database Primer for Molecular Biologists.
J.M. Cherry and S.W. Cartinhour, ACEDB: A Tool for Biological Information.
R. Overbeek and M. Price, The Integration of Curated Biological Databases.