Title: Databases for rRNA gene profiling of microbial communities

Abstract

The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

Inventors:

Ashby, Matthew

Issue Date:

2013-07-02

Research Org.:

Taxon Biosciences, Inc. (Tiburon, CA)

Sponsoring Org.:

USDOE

OSTI Identifier:

1086744

Patent Number(s):

8476016

Application Number:

13/019,045

Assignee:

Taxon Biosciences, Inc. (Tiburon, CA)

Patent Classifications (CPCs):

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

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

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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

G16B20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

C12Q2525/131 - incorporating a restriction site
C12Q1/6869 - Methods for sequencing

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

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

C12Q1/683 - involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
C12Q2521/313 - Type II endonucleases, i.e. cutting outside recognition site
C12Q1/6809 - Methods for determination or identification of nucleic acids involving differential detection

Y - NEW / CROSS SECTIONAL TECHNOLOGIES Y10 - TECHNICAL SUBJECTS COVERED BY FORMER USPC Y10T - TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION

Y10T436/21 - Hydrocarbon

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS

C12Q2600/156 - Polymorphic or mutational markers
C12Q2525/191 - incorporating an adaptor
C12Q1/6888 - for detection or identification of organisms
C12Q2525/151 - repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer

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DOE Contract Number:  

FC36-01GO11016

Resource Type:

Patent

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES