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Nucleic Acids Research 2005 33(Database Issue):D675-D679; doi:10.1093/nar/gki114
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Nucleic Acids Research, 2005, Vol. 33, Database issue D675-D679
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences

Susie M. Stephens*, Jake Y. Chen1,2, Marcel G. Davidson3, Shiby Thomas and Barry M. Trute4

Oracle Corporation, 10 Van de Graaff Drive, Burlington, MA 01803, USA 1 School of Informatics, Indiana University, and 2 Department of Computer and Information Science, School of Science, Purdue University, Indianapolis, IN 46202, USA, 3 Prolexys Pharmaceuticals, 2150 West Dauntless Avenue, Salt Lake City, UT 84116, USA and 4 Oracle Corporation, 200 Oracle Parkway, Redwood Shores, CA 94065, USA

* To whom correspondence should be addressed. Tel: +1 781 744 0372; Fax: +1 781 238 9857; Email: susie.stephens{at}oracle.com

Received September 21, 2004; Revised and Accepted October 20, 2004

As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html

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