Data processing: database and file management or data structures – Database design – Data structure types
Reexamination Certificate
2005-08-16
2005-08-16
Ali, Mohammad (Department: 2167)
Data processing: database and file management or data structures
Database design
Data structure types
C707S793000
Reexamination Certificate
active
06931401
ABSTRACT:
A method and system for conducting sequence searches in a sequence database wherein in one embodiment, the method includes: combining a plurality of query sequences into a combined query sequence; determining a plurality of subdivisions of the sequence database; performing a plurality of searches, wherein each search includes a comparison of the combined query sequence against one of the plurality of subdivisions of the database to produce a plurality of word matches; extending the length of the plurality of word matches to produce a plurality of High-scoring Segment Pairs, combining the plurality of High-scoring Segment Pairs; and producing a plurality of reports, each report representing the highest scoring matches for one of the plurality of query sequences.
REFERENCES:
patent: 6112288 (2000-08-01), Ullner
patent: 6223186 (2001-04-01), Rigault et al.
patent: 6421613 (2002-07-01), Nadimpalli et al.
patent: 6470277 (2002-10-01), Chin et al.
patent: 6691109 (2004-02-01), Bjornson et al.
Altschul et al. “Basic Local Alignment Search Tool” J. Mol. Biol. 215(3):403-410 (1990).
Altschul et al. “Gapped BLAST and PSI-BLAST: New Generation of Protein Database Search Programs” Nucleic Acids Research 25(17):389-3402 (1997).
Benson et al. “GenBank” Nucleic Acids Research 28(1):15-18 (2000).
Bentley. “Multidimensional Binary Search Trees Used for Associative Searching” Communications of the ACM 18(9):509-517 (1975).
Eddy. “Profile Hidden Markov Models” Bioinformatics 14(9):755-763 (1998).
Henikoff et al. “Amino Acid Substitution Matrices from Protein Blocks” Proc. Natl. Acad. Sci. USA 89:10915-10919 (1992).
Henikoff et al. “Performance Evaluation of Amino Acid Substitution Matrices” Proteins 17:49-61 (1993).
<http://www.ncbi.nlm,.nih.gov/Genbank/genbankstats.html> (visited Jul. 30, 2002).
Zhang et al. “Chaining Multiple-Alignment Blocks” J. of Computational Biology 1:217-226 (1994).
Zhang et al. “A Greedy Algorithm for Aligning DNA Sequences” J. of Computational Biology 7(1-2):203-214 (2000).
Altschul et al. “Basic Local Alignment Statistics”Methods in Enzymology266:460-480 (1996).
Gibson Michael A.
Messenger Richard J.
Rieffel Marc A.
Zhang Zheng
Ali Mohammad
Morrison & Foerster / LLP
Paracel, Inc.
LandOfFree
Methods and apparatus for high-speed approximate sub-string... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Methods and apparatus for high-speed approximate sub-string..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Methods and apparatus for high-speed approximate sub-string... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3499304