Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences.
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.
Stephens
Susie M
SM
Oracle Corporation, 10 Van de Graaff Drive, Burlington, MA 01803, USA. susie.stephens@oracle.com
Chen
Jake Y
JY
Davidson
Marcel G
MG
Thomas
Shiby
S
Trute
Barry M
BM
D020816:Amino Acid Motifs; D019295:Computational Biology; D017124:Conserved Sequence; D003628:Database Management Systems; D030541:Databases, Genetic; D006801:Humans; D020539:Sequence Analysis, Protein; D017385:Sequence Homology; D018511:Systems Integration