Data processing: database and file management or data structures – Database design – Data structure types
Reexamination Certificate
2007-06-12
2007-06-12
Smith, Carolyn L. (Department: 1631)
Data processing: database and file management or data structures
Database design
Data structure types
C700S003000, C702S019000
Reexamination Certificate
active
09881234
ABSTRACT:
A method and system of comparing a query and a subject database using a distributed computing platform is disclosed. The databases are divided into data elements having a size within a specified range. All data elements and task definitions are sent to a master CPU of a master-slave distributed computing platform, wherein task definitions comprise at least one comparison parameter, at least one executable comparison element, and a query and a subject data element ID/descriptor. Data elements are sent alternately from query and subject data elements. A task definition is sent for each task from the master CPU to one of a plurality of slave CPUs when all parts of a task definition and data elements referenced by the task definition are available at the master CPU. Data elements are then sent to the slave CPUs for performance of the tasks. Task results for each task are returned to a CPU.
REFERENCES:
patent: 5577249 (1996-11-01), Califano
patent: 5706498 (1998-01-01), Fujimiya et al.
patent: 5862325 (1999-01-01), Reed et al.
patent: 5970500 (1999-10-01), Sabatini et al.
patent: 6303297 (2001-10-01), Lincoln et al.
Altschul et al. Basic Local Alignment Search Tool, 1990, Journal of Molecular Biology, vol. 215, No. 3, pp. 403-410.
Anderson et al. Searching DNA databases for similarities to DNA sequences: when is a match significant?, 1998, Bioinformatics, vol. 14, No. 4, pp. 349-356.
Matsumoto et al., Biological Sequence Compression Algorithms, 2000, Genome Informatics, vol. 11, pp. 43-52.
“Master/slave” definition, Webopedia, on the world wide web at webopedia.com/TERM/M/master—slave.html, 2001, 2 pages.
“Expressed sequence tag” definition, Human Genome Project Information, on the world wide web at ornl.gov/sci/techresources/Human—Genome/glossary/glossary—e.shtml, 2003, 3 pages.
Smith et al. BCM Search Launcher—An Integrated Interface to Molecular Biology Data Base Search And Analysis Services Available on the World Wide Web. 1996, Genome Research, vol. 6, pp. 454-462.
“System” definition, Merriam-Webster online dictionary, on the world wide web at m-w.com/cgi-bin/dictionary?book=Dictionary&va=system, 2004, 2 pages.
“Efficient” definition, online Merriam-Webster dictionary, on the world wide web at m-w.com/cgi-bin/dictionary?book=Dictionary&va=efficient, 2004, 1 page.
Andreson, Isobel & Brass, Andy, “Searching DNA databases for similarities to DNA sequences: when is a match significant?” Bioinformatics, 1998. pp. 349-365, vol. 14, No. 4, University of Manchester, Manchester, United Kingdom.
Toshiko Matsumoto, Kunihiko Sadakane, & Hiroshi Imai, “Biological Sequence Compression Algorithms” General Informatics, 2000, pp. 43-52, vol. II, Tokyo, Japan.
Karlin, Samuel, et al., “Applications and Statistics for Multiple High-Scoring Segments in Molecular Sequences,” Proc. Natl. Acad. Sci. USA, vol. 90, pp. 5873-5877, Jun. 1993.
Altschul, Stephen F., et al., “Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs,” Nucleic Acids Research, vol. 25, No. 17, 1997.
BLAST 2.0 Release Notes (revised May 25, 1998), http://pbil.univ-lyon1.fr/BLAST.description.html.
Varre, Jean-Stephane, et al., “Transformation Distances: A Family of Dissimilarity Measures Based on Movements of Segments,” Bioinformatics, vol. 15, No. 3, pp. 194-202, 1999.
Brudno, Michael, et al., “Fast and Sensitive Multiple Alignment of Large Genomic Sequences,” BMC Bioinformatics, Dec. 23, 2003.
Blair Douglas M.
Grefenstette John J.
Lucien Dustin M.
Nash H. Hadon
Newfield Dale I.
Parabon Computation, Inc.
Roberts Mardula & Wertheim LLC
Smith Carolyn L.
LandOfFree
Apparatus and method for providing sequence database comparison does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Apparatus and method for providing sequence database comparison, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Apparatus and method for providing sequence database comparison will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3819878