WO2005029280A3 - Performing sequence analysis as a multipart plan storing intermediate results as a relation - Google Patents

Performing sequence analysis as a multipart plan storing intermediate results as a relation Download PDF

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Publication number
WO2005029280A3
WO2005029280A3 PCT/US2004/030700 US2004030700W WO2005029280A3 WO 2005029280 A3 WO2005029280 A3 WO 2005029280A3 US 2004030700 W US2004030700 W US 2004030700W WO 2005029280 A3 WO2005029280 A3 WO 2005029280A3
Authority
WO
WIPO (PCT)
Prior art keywords
sequence analysis
multipart
relation
intermediate results
storing intermediate
Prior art date
Application number
PCT/US2004/030700
Other languages
French (fr)
Other versions
WO2005029280A2 (en
Inventor
Barry M Zane
Sanjay G Dixit
Venkannababu Tammisetti
Original Assignee
Netezza Corp
Barry M Zane
Sanjay G Dixit
Venkannababu Tammisetti
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Netezza Corp, Barry M Zane, Sanjay G Dixit, Venkannababu Tammisetti filed Critical Netezza Corp
Publication of WO2005029280A2 publication Critical patent/WO2005029280A2/en
Publication of WO2005029280A3 publication Critical patent/WO2005029280A3/en

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Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/24—Querying
    • G06F16/245—Query processing
    • G06F16/2453—Query optimisation
    • G06F16/24534—Query rewriting; Transformation
    • G06F16/24542—Plan optimisation
    • G06F16/24544—Join order optimisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/70—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/24—Querying
    • G06F16/242—Query formulation
    • G06F16/2433—Query languages
    • G06F16/2448—Query languages for particular applications; for extensibility, e.g. user defined types
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/24—Querying
    • G06F16/245—Query processing
    • G06F16/2453—Query optimisation
    • G06F16/24534—Query rewriting; Transformation
    • G06F16/24547—Optimisations to support specific applications; Extensibility of optimisers
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/24—Querying
    • G06F16/245—Query processing
    • G06F16/2455—Query execution
    • G06F16/24553—Query execution of query operations
    • G06F16/24558—Binary matching operations
    • G06F16/2456—Join operations
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/24—Querying
    • G06F16/245—Query processing
    • G06F16/2458—Special types of queries, e.g. statistical queries, fuzzy queries or distributed queries
    • G06F16/2474—Sequence data queries, e.g. querying versioned data
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S707/00—Data processing: database and file management or data structures
    • Y10S707/99931—Database or file accessing

Abstract

A usage model and the underlying technology used to provide sequence analysis as part of a relational database system. Included components include the semantic and syntactic integration of the sequence analysis with an existing query language, the storage methods for the sequence data, and the design of a multipart execution scheme that runs the sequence analysis as part of a potentially larger database query, especially using parallel execution techniques.
PCT/US2004/030700 2003-09-19 2004-09-17 Performing sequence analysis as a multipart plan storing intermediate results as a relation WO2005029280A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US50444303P 2003-09-19 2003-09-19
US60/504,443 2003-09-19

Publications (2)

Publication Number Publication Date
WO2005029280A2 WO2005029280A2 (en) 2005-03-31
WO2005029280A3 true WO2005029280A3 (en) 2006-08-10

Family

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Family Applications (2)

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PCT/US2004/030417 WO2005028627A2 (en) 2003-09-19 2004-09-17 Performing sequence analysis as a relational join
PCT/US2004/030700 WO2005029280A2 (en) 2003-09-19 2004-09-17 Performing sequence analysis as a multipart plan storing intermediate results as a relation

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PCT/US2004/030417 WO2005028627A2 (en) 2003-09-19 2004-09-17 Performing sequence analysis as a relational join

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US (5) US7702610B2 (en)
WO (2) WO2005028627A2 (en)

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