WO2014081882A3 - Systems and methods for analyzing coding sequences based on genetic distances - Google Patents

Systems and methods for analyzing coding sequences based on genetic distances Download PDF

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Publication number
WO2014081882A3
WO2014081882A3 PCT/US2013/071089 US2013071089W WO2014081882A3 WO 2014081882 A3 WO2014081882 A3 WO 2014081882A3 US 2013071089 W US2013071089 W US 2013071089W WO 2014081882 A3 WO2014081882 A3 WO 2014081882A3
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WO
WIPO (PCT)
Prior art keywords
coding sequences
systems
methods
zero
sequences based
Prior art date
Application number
PCT/US2013/071089
Other languages
French (fr)
Other versions
WO2014081882A2 (en
Inventor
Raul Rabadan
Joseph M. CHAN
Original Assignee
The Trustees Of Columbia University In The City Of New York
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 The Trustees Of Columbia University In The City Of New York filed Critical The Trustees Of Columbia University In The City Of New York
Publication of WO2014081882A2 publication Critical patent/WO2014081882A2/en
Publication of WO2014081882A3 publication Critical patent/WO2014081882A3/en

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Classifications

    • 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
    • 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
    • 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

Abstract

Genetic distances between coding sequences of genomes are used to analyze sets of genomes. Genomic surveillance can be analyzed by identifying a proportion of coding sequences less than some filtration value from a closest ancestor, or by converting the coding sequences into a point cloud representation and using a persistence homology technique to find the zero-dimensional Betti number. A non¬ zero value of Betti numbers greater than zero can also indicate that nonvertical genetic exchanges have occurred.
PCT/US2013/071089 2012-11-20 2013-11-20 Systems and methods for analyzing coding sequences based on genetic distances WO2014081882A2 (en)

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US201261728694P 2012-11-20 2012-11-20
US201261728704P 2012-11-20 2012-11-20
US61/728,694 2012-11-20
US61/728,704 2012-11-20
US201361749802P 2013-01-07 2013-01-07
US61/749,802 2013-01-07

Publications (2)

Publication Number Publication Date
WO2014081882A2 WO2014081882A2 (en) 2014-05-30
WO2014081882A3 true WO2014081882A3 (en) 2014-07-17

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Application Number Title Priority Date Filing Date
PCT/US2013/071089 WO2014081882A2 (en) 2012-11-20 2013-11-20 Systems and methods for analyzing coding sequences based on genetic distances

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WO (1) WO2014081882A2 (en)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB2539637A (en) * 2015-05-14 2016-12-28 Greenfield Daniel System and method for transforming and compressing genomics data
EP3298524A4 (en) * 2015-05-22 2019-03-20 CSTS Health Care Inc. Thermodynamic measures on protein-protein interaction networks for cancer therapy
GB2543068A (en) 2015-10-06 2017-04-12 Fonleap Ltd System for generating genomics data, and device, method and software product for use therein

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20070225918A1 (en) * 2003-06-19 2007-09-27 Khalid Sayood System and Method for Sequence Distance Measure for Phylogenetic Tree Construction
US20100169343A1 (en) * 2008-12-30 2010-07-01 Expanse Networks, Inc. Pangenetic Web User Behavior Prediction System
US20100317034A1 (en) * 2005-02-21 2010-12-16 The Government of the United States of America as represented by the Secretary of the Primate t-lymphotropic viruses
US8315816B2 (en) * 2005-02-16 2012-11-20 Genetic Technologies Limited Methods of genetic analysis involving the amplification of complementary duplicons

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20070225918A1 (en) * 2003-06-19 2007-09-27 Khalid Sayood System and Method for Sequence Distance Measure for Phylogenetic Tree Construction
US8315816B2 (en) * 2005-02-16 2012-11-20 Genetic Technologies Limited Methods of genetic analysis involving the amplification of complementary duplicons
US20100317034A1 (en) * 2005-02-21 2010-12-16 The Government of the United States of America as represented by the Secretary of the Primate t-lymphotropic viruses
US20100169343A1 (en) * 2008-12-30 2010-07-01 Expanse Networks, Inc. Pangenetic Web User Behavior Prediction System

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
CHAN ET AL.: "Quantifying pathogen surveillance using temporal genomic data. art. e00524-12", MBIO., vol. 4, no. 1, 29 January 2013 (2013-01-29), pages 1 - 10 *
LIVIU ET AL.: "Estimating Similarities in DNA Strings Using the Efficacious Rank Distance Approach.", SYSTEMS AND COMPUTATIONAL BIOLOGY - BIOINFORMATICS AND COMPUTATIONAL MODELING., August 2011 (2011-08-01), pages 122 - 138, Retrieved from the Internet <URL:http://www.zums.ac.ir/files/research/site/ebooks/Numerical%20Analysis%20and%20Scientific%20Computing/Systems_and_Computational_Biology_-_Bioinformatics_and_Computational_Modeling.pdf> [retrieved on 20140331] *
SMITH ET AL.: "Origin and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.", NATURE, vol. 459, 2009, pages 1122 - 1125 *

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