CA2370539A1 - System and method for notating polymers - Google Patents

System and method for notating polymers Download PDF

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Publication number
CA2370539A1
CA2370539A1 CA002370539A CA2370539A CA2370539A1 CA 2370539 A1 CA2370539 A1 CA 2370539A1 CA 002370539 A CA002370539 A CA 002370539A CA 2370539 A CA2370539 A CA 2370539A CA 2370539 A1 CA2370539 A1 CA 2370539A1
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CA
Canada
Prior art keywords
polymer
properties
computer
data structure
chemical units
Prior art date
Legal status (The legal status 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 status listed.)
Granted
Application number
CA002370539A
Other languages
French (fr)
Other versions
CA2370539C (en
Inventor
Ganesh Venkataraman
Zachary Shriver
Rahul Raman
Ram Sasisekharan
Nishla Keiser
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Massachusetts Institute of Technology
Original Assignee
Massachusetts Institute Of Technology
Ganesh Venkataraman
Zachary Shriver
Rahul Raman
Ram Sasisekharan
Nishla Keiser
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 Massachusetts Institute Of Technology, Ganesh Venkataraman, Zachary Shriver, Rahul Raman, Ram Sasisekharan, Nishla Keiser filed Critical Massachusetts Institute Of Technology
Priority to CA2643162A priority Critical patent/CA2643162C/en
Publication of CA2370539A1 publication Critical patent/CA2370539A1/en
Application granted granted Critical
Publication of CA2370539C publication Critical patent/CA2370539C/en
Anticipated expiration legal-status Critical
Expired - Lifetime legal-status Critical Current

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Classifications

    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K1/00General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/30Data warehousing; Computing architectures
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/40Encryption of genetic data
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16CCOMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
    • G16C20/00Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
    • G16C20/20Identification of molecular entities, parts thereof or of chemical compositions
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00ICT programming tools or database systems specially adapted for bioinformatics
    • YGENERAL 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
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10STECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S707/00Data processing: database and file management or data structures
    • Y10S707/99931Database or file accessing
    • Y10S707/99933Query processing, i.e. searching
    • Y10S707/99936Pattern matching access
    • YGENERAL 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
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10STECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S707/00Data processing: database and file management or data structures
    • Y10S707/99941Database schema or data structure
    • Y10S707/99943Generating database or data structure, e.g. via user interface

Abstract

A data structure, tangibly embodied in a computer-readable medium, representing a polymer of chemical units is disclosed. The data structure includes an identifier including a plurality of fields for storing values corresponding to properties of the polymer. In one embodiment, the fields are capable of storing binary values.
The polymer may, for example, be a polysaccharide and the chemical units may be saccharides. A computer-implemented method for determining whether properties of a query sequence of chemical units match properties of a polymer of chemical units. The query sequence is represented by a first data structure, tangibly embodied in a computer-readable medium, including an identifier including a plurality of bit fields for storing values corresponding to properties of the query sequence. The polymer is represented by a second data structure, tangibly embodied in a computer-readable medium, including an identifier including a plurality of bit fields for storing values corresponding to properties of the polymer. The invention also relates to methods of sequencing polymers such as nucleic acids, polypeptides and polysaccharides and methods for identifying a polysaccharide-protein interaction. The invention also involves a notational system referred to as Property Encoded Nomenclature.
CA002370539A 1999-04-23 2000-04-24 System and method for notating polymers Expired - Lifetime CA2370539C (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
CA2643162A CA2643162C (en) 1999-04-23 2000-04-24 Polymer identification, compositional analysis and sequencing, based on property comparison

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
US13074799P 1999-04-23 1999-04-23
US13079299P 1999-04-23 1999-04-23
US60/130,747 1999-04-23
US60/130,792 1999-04-23
US15994099P 1999-10-14 1999-10-14
US15993999P 1999-10-14 1999-10-14
US60/159,939 1999-10-14
US60/159,940 1999-10-14
PCT/US2000/010990 WO2000065521A2 (en) 1999-04-23 2000-04-24 System and method for polymer notation

Related Child Applications (1)

Application Number Title Priority Date Filing Date
CA2643162A Division CA2643162C (en) 1999-04-23 2000-04-24 Polymer identification, compositional analysis and sequencing, based on property comparison

Publications (2)

Publication Number Publication Date
CA2370539A1 true CA2370539A1 (en) 2000-11-02
CA2370539C CA2370539C (en) 2009-01-06

Family

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Family Applications (2)

Application Number Title Priority Date Filing Date
CA002370539A Expired - Lifetime CA2370539C (en) 1999-04-23 2000-04-24 System and method for notating polymers
CA2643162A Expired - Lifetime CA2643162C (en) 1999-04-23 2000-04-24 Polymer identification, compositional analysis and sequencing, based on property comparison

Family Applications After (1)

Application Number Title Priority Date Filing Date
CA2643162A Expired - Lifetime CA2643162C (en) 1999-04-23 2000-04-24 Polymer identification, compositional analysis and sequencing, based on property comparison

Country Status (5)

Country Link
US (8) US7412332B1 (en)
EP (1) EP1190364A2 (en)
JP (1) JP4824170B2 (en)
CA (2) CA2370539C (en)
WO (1) WO2000065521A2 (en)

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US6597996B1 (en) 2003-07-22
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US20070066769A1 (en) 2007-03-22
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