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An object-oriented genetics information system

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Ernest RetzelAuthors Info & Claims

SAC '93: Proceedings of the 1993 ACM/SIGAPP symposium on Applied computing: states of the art and practice

Pages 641 - 651

https://doi.org/10.1145/162754.167189

Published: 01 March 1993 Publication History

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References

[1]

Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. Basic Alignment Search Tool, Journal of Molecular Biology, vol. 215, pp. 403-410

Crossref

Google Scholar

[2]

Altschul, Stephen F. Amino Acid Substitution Matrices from an Information Theoretic Prospective, Journal of Molecular Biology, vol. 219, pp. 555-565, 1991.

Crossref

Google Scholar

[3]

Bays, J.C., Ph.D., The Complete PATRICIA, Ph.D. dissertation, U. of Oklahoma, 1974.

Digital Library

Google Scholar

[4]

Burks, Christian, et al. { 1990}. GenBank: Current Status and Future Directions, Methods in Enzymology, Vol. 183, Academic Press

Crossref

Google Scholar

[5]

Durbin, Richard and Jean Tlerry-Mieg, acexlb - A C. Elegans Database, User's Guide, installation Guide, and Configuration Guide, March, 1992.

Google Scholar

[6]

Fickett, J.W., M.J. Cinkosky, C. Burks, P.E. Hempfner, D. Nelson, R.M. Pecherer, P. Sgro, DM. Sorenson, R.D. Sutherland, and B.C. Yantis {1991} Human Genome Information Resource, LANL Technical Report, obtained through personal commumcation.

Google Scholar

[7]

Fields, C. A. and C. A. Soderlund. gm: A Practical Tool for Automating DNA Sequence Analysis, Computer Applications in the Biological Sciences (CABIOS), vol 6, pp. 263-270, 1990.

Google Scholar

[8]

GDE, Genetic Data Environment, version 2.0 Users Guide, Harvard Genome Laboratory, 1992.

Google Scholar

[9]

Relational Schema of Genbank Database {1992}. personal communication with Los Alamos National Laboratory.

Google Scholar

[10]

Gonnet, Gaston H., Mark A. Cohen, and Stephen A.Benner. Exhaustive Matching of the Entire Protein Sequence Database, Science, vol. 256, pp. 1443-1445, June 5, 1992.

Crossref

Google Scholar

[11]

Gorry, G. Anthony, Kevin B. Long, Andrew M. Burger, Cynthia P. Jung, Barry D. Meyer. The Virtual Notebook System: An Architecture for Collaborative Work, journal of Organizational Computing, 1 (3), pp. 233-250, 1991.

Crossref

Google Scholar

[12]

Gotoh O., An Improved Algorithm for Matching Biological Sequences, J. Mol. Biol. (1982). 162, 705-708.

Crossref

Google Scholar

[13]

Human Genome 1991-1992 Program Report, U.S. Dept. of Energy publication DOE~R-0544P, June, 1992.

Google Scholar

[14]

Hunkapiller, Tim, Leroy Hood, Ed Chen, Michael Waterman. BISP: VLSI Solutions to Sequence-Comparison Problems, Human Genome 1991-1992 Program Report, U.S. Dept. of Energy publication DOE~R-0544P, June, 1992. pp. 143

Google Scholar

[15]

1TASCA Distributed Object Database Management System User Manual, Release 2.0, Itasca Systems, Inc., 1992

Google Scholar

[16]

Johnston, William, Suzanna Lewis, Victor Markowitz, John McCarthy, Frank Olken, and Manfred Zorn { 1991}. The Chromosome Information System, Lawrence Berkeley Laboratory Technical Report 29675, May 17, 1991

Google Scholar

[17]

Karlin, Samuel and Stephen F. Altschul. Methods for assessing the statistical significance of molecular sequence features using general scoring schemes, Proceedings of the National Academy of Sciences USA, Vol. 87, pp. 2264-2268, 1990.

Crossref

Google Scholar

[18]

Kim, Won. Introduction to Object-Oriented Databases, MIT Press, 1991.

Digital Library

Google Scholar

[19]

Hughes, J.G. Object-Oriented Databases, Prentice Hall International, Hemel Hempstead, England, 1991.

Digital Library

Google Scholar

[20]

Kim, Won, et. al. "Features of the ORION Object-Oriented Database System," Object-Oriented Concepts, Applications. and Databases, ed. W. Kim and F. Lochovsky, Addison-Wesley, 1989.

Digital Library

Google Scholar

[21]

Kim, Won. "Architecture of the ORION Next-Generation Database System,", IEEE Transactions on Knowledge and Data Engineering, March 1990.

Digital Library

Google Scholar

[22]

McCreight, Edward M., A Space-Economical Suffix Tree Construction Algorithm, JACM, 23(2), April, 1976, pp 262-272.

Digital Library

Google Scholar

[23]

Needleman, S.B. & Wtmsch C.D., (1970). J. Mol. Biol. 48, 443-453

Google Scholar

[24]

Pearson, W. R. and D. J. Lipman. Improved Tools for Biological Sequence Analysis, Proceedings of the National Academy of Sciences USA, Vol. 85, pp. 2~ 2448, 1988.

Google Scholar

[25]

Pearson, W.R. Rapid and Sensitive Sequence Comparison with FASTP and FASTA, Methods in Enzymology, vol 183, pp. 63-98, 1990.

Crossref

Google Scholar

[26]

Powell, Patrick A., Using and Constructing the Sufftx Tree Index Structure, U. of Minnesota Computer Science Department, Technical Report TR 89-90

Google Scholar

[27]

Powell, P.A., P. Bieganski, E. Shoop {1989}. Xll - Based Tools for Network Access to and Comparison of DNA Sequence Data. Presentation at MacroMolecules, Genes and Computers, Chapter Two, Watervi!le Valley, New Hampshire.

Google Scholar

[28]

P.A. Powell {1990}. FASTSIM: A New Algorithm for Rapid Sequence Similarity Determination. Presentation at Amencan Medical Informatics Association First Annual Research Conference: Computers, Molecular Biology and Medicine. Snowbird, Utah.

Google Scholar

[29]

Shin, Dong-Guk, Changwan Lee, Jmghui Zhang, Kenneth E. Rudd, and Claire M. Berg. Redesigning, Implementing, and Integrating Escherichia Coli Genome Software Tools with an Object-Oriented Database System, Computer Applications in the Biological Sciences (CABIOS), vol.8, no. 3, pp. 227-238, 1992.

Google Scholar

[30]

Shoop, E., E.E Retzel, P.A. Powell, P. Bieganski and S. Kemp {1990}. The MOLBIO Project: A System for Access, Comparison and Display of Molecular Information. Presentation at American Medical Informatics Association First Annual Research Conference: Computers, Molecular Biology and Medicine. Snowbird, Utah.

Google Scholar

[31]

Waterman, M.S., Smith, T.F. & Beyer, W.A. (1976). Advan. MAth. 20, 367-387.

Google Scholar

[32]

Zoeller, Randal and Douglas Barry. Dynamic Self- Configuring Method, v for Graphical Presentation of ODBMS Objects, ProceeAings, gth International Conference on Data Engineering, IEEE Computer Society Press, 1992, pp. 136-143.

Digital Library

Google Scholar

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Shoop Carlis Retzel (1994)Automating and streamlining inference of function of plant ESTs within a data analysis systemProceedings of the Twenty-Seventh Hawaii International Conference on System Sciences HICSS-9410.1109/HICSS.1994.323591(47-48)Online publication date: 1994
https://doi.org/10.1109/HICSS.1994.323591

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An object-oriented genetics information system

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SAC '93: Proceedings of the 1993 ACM/SIGAPP symposium on Applied computing: states of the art and practice

March 1993

804 pages

ISBN:0897915674

DOI:10.1145/162754

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 01 March 1993

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SAC93: 1993 Symposium on Applied Computing

February 14 - 16, 1993

Indiana, Indianapolis, USA

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Shoop Carlis Retzel (1994)Automating and streamlining inference of function of plant ESTs within a data analysis systemProceedings of the Twenty-Seventh Hawaii International Conference on System Sciences HICSS-9410.1109/HICSS.1994.323591(47-48)Online publication date: 1994
https://doi.org/10.1109/HICSS.1994.323591

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Recommendations

The Korea Brassica Genome Project: A glimpse of the Brassica genome based on comparative genome analysis with Arabidopsis: Conference Papers

New computational tools for Brassica genome research: Conference Reviews

A graphical user interface for object-oriented database