An object-oriented genetics information system

Elizabeth Snoop, Jaideep Srivastava, Paul Bieganski, John Riedl, Ernest Retzel

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Sequence data is being produced by genomic sequencing laboratories at ever-increasing rates, making it impossible for individual researchers to keep track of all the new data that might affect their research. Computer systems are needed so that researchers can access this data. The systems must support high-level interfaces that communicate in the language of the researchers, database systems that guarantee availability and consistency of the data, and powerful search systems that rapidly scan for similarities between sequences. We have developed a prototype system that includes a graphical user interface, an object-oriented database management system, and high-performance similarity search algorithms. The prototype has the potential to increase researchers' productivity by automating entry of annotated sequence fragments as they are produced by sequencing machines, storing the fragments in the database, and automatically producing and displaying similarity search results of new sequences against the large public sequence databases GenBank and PIR. This paper describes the prototype, discusses the benefits of object-oriented databases for complex and changing sequence data, and presents an object-oriented schema for genetic information. Graphical tools for annotating sequences, storing them in the database, automating similarity searches, and viewing similarity search results are presented. A new suffix treebased data structure that supports rapid similarity searches on sequence data is introduced. Finally, future plans for the system are discussed.

Original languageEnglish
Title of host publicationProceedings of the 1993 ACM/SIGAPP Symposium on Applied Computing
Subtitle of host publicationStates of the Art and Practice, SAC 1993
EditorsEd Deaton, George Hedrick, K.M. George, Hal Berghel
PublisherAssociation for Computing Machinery
Pages641-651
Number of pages11
ISBN (Electronic)0897915674
DOIs
Publication statusPublished - 1 Mar 1993
Event1993 ACM/SIGAPP Symposium on Applied Computing: States of the Art and Practice, SAC 1993 - Indianapolis, United States
Duration: 14 Feb 199316 Feb 1993

Publication series

NameProceedings of the ACM Symposium on Applied Computing
VolumePart F129680

Other

Other1993 ACM/SIGAPP Symposium on Applied Computing: States of the Art and Practice, SAC 1993
CountryUnited States
CityIndianapolis
Period14/2/9316/2/93

Keywords

  • Computational molecular biology
  • Genome sequencing
  • Graphical user interface
  • Object-oriented database
  • Suffix tree

ASJC Scopus subject areas

  • Software

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  • Cite this

    Snoop, E., Srivastava, J., Bieganski, P., Riedl, J., & Retzel, E. (1993). An object-oriented genetics information system. In E. Deaton, G. Hedrick, K. M. George, & H. Berghel (Eds.), Proceedings of the 1993 ACM/SIGAPP Symposium on Applied Computing: States of the Art and Practice, SAC 1993 (pp. 641-651). (Proceedings of the ACM Symposium on Applied Computing; Vol. Part F129680). Association for Computing Machinery. https://doi.org/10.1145/162754.167189