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.
* The field of automation in DAN sequencing and analysis is rapidly moving. Hovever, as the technology becomes commonplace, those applying the techniques involved to their research fields need a text which both expands on the protocols supplied by manufacturers with their instruments and explains how to utilise the data produced. This book fulfils those needs, reviews the history of the art and provides pointers to future development.
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