Design and implementation of a string database query language

  • Authors:

  • Gösta Grahne;Raul Hakli;Matti Nykänen;Hellis Tamm;Esko Ukkonen

  • Affiliations:

  • Department of Computer Science, Concordia University, Sir George Williams Campus, 1455 De Maisonneuve Blvd. West, LB 903 11, Montreal, QC, Canada H3G 1M8;Department of Computer Science, University of Helsinki, P.O. Box 26, Teollisuuskatu 23, Helsinki 00014, Finland;Department of Computer Science, University of Helsinki, P.O. Box 26, Teollisuuskatu 23, Helsinki 00014, Finland;Department of Computer Science, University of Helsinki, P.O. Box 26, Teollisuuskatu 23, Helsinki 00014, Finland;Department of Computer Science, University of Helsinki, P.O. Box 26, Teollisuuskatu 23, Helsinki 00014, Finland

  • Venue:
  • Information Systems - Special issue: Data management in bioinformatics
  • Year:
  • 2003

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Abstract

Current data management and information retrieval systems lack advanced string processing capabilities needed in string-oriented application areas like computational molecular biology. Several theoretical models for string processing have been proposed but they either have not been implemented in practice or the implementations are too restricted or platform-dependent to be generally useful. In this article, we introduce the language Alignment Declarations designed for string querying and restructuring. The language extends the capabilities of existing database query languages by allowing the user to define database predicates that express structural properties of strings (e.g. containment of certain patterns) or relations between several strings (e.g. similarity measures). These predicates can be created and executed within the same database session and also stored for later sessions. We also describe the design and implementation of a working system.