The Genome Data Base V6
Kenneth H. Fasman, Stanley I. Letovsky, Peter Li, Robert W. Cottingham, and David T. Kingsbury
Data Acquisition and Curation in the Genome Data Base V6
Michael A. Chipperfield, Christopher J. Porter, and C. Conover Talbot, Jr.
A Revised Schema for the Genome Data Base V6
Kenneth H. Fasman, Stanley I. Letovsky, Peter Li, Krishna Palaniappan, Michael A. Chipperfield, Christopher J. Porter, John M. Campbell, Edward W. Kraska, Sue E. Borchardt, and Deborah J. Schneider
Improved Map Representation for the Genome Database V6
Stanley I. Letovsky, Kenneth H. Fasman, and Peter Li
An Extensible Object Broker for the Genome Data Base V6
Peter Li, David Waldo, Stuart V. Pineo, and John M. Campbell
User Interfaces for Querying, Editing, and Viewing the Genome Data Base V
Sue E. Borchardt, Stanley I. Letovsky, Kenneth H. Fasman, Laurie C. Kramer, Karen J. Phipps, Lita A. Kearney, Deborah J. Schneider, and Thomas C. Emmel
The Genome Sequence Database (GSDB): Meeting the Challenge of Genome-scale Sequencing
Gifford Keen, Jillian Burton, David Crowley, Emily Dickinson, Ada Espinosa-Lujan, Ed Franks,
Carol Harger, Mo Manning, Shelley March, Mia McLeod, John O'Neill, Alicia Power, Maria
Pumilia, David Rider, John Rorlich, Jolene Schwertferger, Linda Smyth, Nina Thayer, Charles
Troup, and Chris Fields
Requirements Analysis and Functional Specification for a Sequencing Information Management
System
Chris Fields, Gifford Keen, Shelley March, David Rider, John Rorlich, and Charles Troop
The Role of Integrated Software and Databases in Genome Sequence Interpretation and
Metabolic Reconstruction
Terry Gaasterland, Natalia Maltsev, Ross Overbeek, and Evgeni Selkov
3DBase - A Macromolecular Structure Database
E. E. Abola, J. Prilusky, N. O. Manning, and J. L. Sussman
TIGR Database (TDB): Integrated Biological Databases to Support Research in Gene
Expression, Protein Families and Genome Evolution
Anthony R. Kerlavage, Mark D. Adams, Judith Blake, Carol Bult, Rebecca Clayton, Lisa
FitzGerald, Anna Glodek, Michael Heaney, Robert Shirley, Granger Sutton, Owen White, and J.
Craig Venter
Data Management For The Resource For Molecular Cytogenetics
Manfred D. Zorn and Jenny E. Marstaller
A Database System to Support Genome Mapping
Mark Graves
A Flexible Database Schema for Large-Scale Physical Mapping and Sequencing Across Multiple
Genomes
Tom Slezak, Mark Wagner, and T. Mimi Yeh.
The BCM/UH Network Server Core and Search Launcher
Daniel B. Davison, Brent A. Wiese, Istvan Ladunga, Kim C. Worley and Randall F. Smith
Enhanced Resources for Accessing Genetic and Biological Information via the World Wide Web
Amy K. Voltz and Kenneth H. Fasman
A Graphical Ad Hoc Query Interface Capable of Accessing Heterogeneous Public
Genome Databases
Joseph Leone, Dong-Guk Shin
On-Demand Integration of Biological Data
J. Crabtree, L. Wong, P. Buneman, S.B. Davidson, and C. Overton
GRAIL-genQuest: A Comprehensive Computational Framework for DNA Sequence Analysis
Ruth Ann Manning and Bjorn E.F. Mossberg
A Tool for Reengineering Large Databases
Mark C. Wagner, Shannon Waller, T. Mimi Yeh, and Thomas R. Slezak.
Submitdata: Data Submission to Public Genomic Databases
Manfred D. Zorn
Providing Object-Oriented Interfaces for Molecular Biology Databases
Victor M. Markowitz, I-Min A. Chen, Anthony Kosky, and Ernest Szeto
Version 4 of the OPM Data Management Tools: Enhanced Support for Molecular Biology
Databases
Victor M. Markowitz, I-Min A. Chen, Ernest Szeto, and Jia-Lin N. Chen
Querying Heterogenous Molecular Biology Database
Victor M. Markowitz, I-Min A. Chen, Anthony Kosky, and Ernest Szeto
SPACE: A Flexible Database and Analysis Tool For Genomic Sequence Reconstruction and
Multi Species Mapping
Arun Aggarwal, Sam Pitluck, Frank Eeckman
Transforming Molecular Biology Databases Using Morphase
S.B. Davidson, A. Kosky, C. Overton, and P. Buneman
Providing Database Access to Structured Files
W. Fan, P. Buneman, S.B. Davidson, and C. Overton
A Freely Sharable Software Component to Manage Genome-Application Data
Steve Rozen, John Lehman, Lincoln Stein, and Nathan Goodman
Informatics Support for Mapping in Mouse-Human Homology Regions
Sergey Petrov, Manesh Shah, Loren Hauser, Richard Mural, and Edward Uberbacher
Automail: an Automated System for Managing E-mail Queries to Servers
Elaine Best and Joe Gatewood
System Design of The Genome Topographer
S. Cozza, D. Cuddihy, R. Iwasaki, M. Mallison, C. Reed, J. Salit, A. Tracy, and T. Marr.
Layout Tools for Clone End-Sequence Sampling Contigs
Guochun Xie, Michael L. Engle, and Christian Burks
Software Support for High-Throughput Sequence Reconstruction
Charles Lawrence, Victor Solovyev, Ellen Bergeman, and Pam Culpepper
A Unix-based Graphical Editing Tool for Shotgun DNA Sequence Assemblies
Chris Abajian, David Gordon, Leroy Hood, and Phil Green.
Combinatorial Aspects of Multiple-Complete-Digest Restriction Mapping
Richard M. Karp and Geoffrey Zweig
Hopper: A Prototype for Data Flow in Large-Scale DNA Sequencing
Todd M. Smith, Chris Abajian, and Leroy Hood
Qview: A Software Tool for the Quantitative Analysis of Protocol Success, Base-calling
Algorithms and Quality Control for Large-scale Sequencing Projects
James N. Labrenz and Tim Hunkapiller
An Information Management System for DNA Sequencing
Arthur Kobayashi, David J. Ow, T. Mimi Yeh, Mark C. Wagner, and Thomas
R. Slezak.
Towards Automatic Assembly for the Directed Sequencing Strategy
Samuel Pitluck, Arun Aggarwal, Frank Eeckman, and Eugene Veklerov
A Workbench for Sequence Annotation and Browsing
Nomi L. Harris and Frank H. Eeckman
A Customizable Software System for Fragment Assembly
Gene Myers and Susan Larson
Towards completely automated sequence assembly
Phil Green
TIGR Assembler:A New Tool for Assembling Large Shotgun Sequencing
Projects
Granger G. Sutton, Owen White, Mark D. Adams, and Anthony R. Kerlavage
Analysis and Annotation of Nucleic Acid Sequence
David J. States, Ron Cytron, Pankaj Agarwal, and Hugh Chou
Statistical Interpretation of Aligned Sequences Related by Evolution
William J. Bruno
Generalized HMM's and the Analysis of DNA Sequences
Catherine A. Macken and Kevin P. Murphy
Sampling Based Methods for Estimation of DNA Sequence Accuracy
Gary Churchill and Betty Lazareva
Identification, Organization and Analysis of Mammalian Repetitive DNA
Jerzy Jurka
Novel Neural Networks for Functional Site Prediction on Large Scale Sequences
Martin G. Reese, Nomi L. Harris, and Frank H. Eeckman
Languages, Automata, Interfaces, and Macromolecules
David B. Searls
Algorithms in Support of the Human Genome Project
Dan Gusfield, Jim Knight, Kevin Murphy, Paul Stelling, and Lushen Wang
A New Technique for Detecting Coding DNA Sequences
David C. Torney, Clive C. Whittaker, and Guochun Xie
Gene Recognition, Modeling, and Homology Search in GRAIL and genQuest
Ying Xu, Manesh Shah, J. Ralph Einstein, Sherri Matis, Xiaojun Guan, Sergey Petrov, Loren Hauser, Richard J. Mural, and Edward C. Uberbacher
Prediction of Coding Regions and Promoters in Genomic DNA
Gary D. Stormo
Spliced Alignment: a New Approach to Gene Recognition
Mikhail S. Gelfand, Andrey A. Mironov, and Pavel A. Pevzner
A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA
David Kulp, David Haussler, Martin Reese, and Frank Eeckman
Fast Protein Folding in the Hydrophobic-hydrophilic Model Within Three-eighths of Optimal
William E. Hart and Sorin Istrail
Smith-Waterman Transformable Array Search Engine Yields Supercomputer Performance on PCS
and Unix Workstations
James W. Lindelien, Robert Farrington, and Betty Tjandra