EP3259590A4 - Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform - Google Patents

Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform Download PDF

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Publication number
EP3259590A4
EP3259590A4 EP16753186.2A EP16753186A EP3259590A4 EP 3259590 A4 EP3259590 A4 EP 3259590A4 EP 16753186 A EP16753186 A EP 16753186A EP 3259590 A4 EP3259590 A4 EP 3259590A4
Authority
EP
European Patent Office
Prior art keywords
apparatuses
integrated circuit
processing platform
circuit processing
methods executed
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.)
Withdrawn
Application number
EP16753186.2A
Other languages
German (de)
French (fr)
Other versions
EP3259590A1 (en
Inventor
Pieter Van Rooyen
Michael Ruehle
Robert J. Mcmillen
Mark Hahm
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.)
Edico Genome Corp
Original Assignee
Edico Genome Corp
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 Edico Genome Corp filed Critical Edico Genome Corp
Publication of EP3259590A1 publication Critical patent/EP3259590A1/en
Publication of EP3259590A4 publication Critical patent/EP3259590A4/en
Withdrawn legal-status Critical Current

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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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • 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
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/30—Data warehousing; Computing architectures

Landscapes

  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
EP16753186.2A 2015-02-20 2016-02-19 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform Withdrawn EP3259590A4 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201562119059P 2015-02-20 2015-02-20
US201562127232P 2015-03-02 2015-03-02
PCT/US2016/018765 WO2016134310A1 (en) 2015-02-20 2016-02-19 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform

Publications (2)

Publication Number Publication Date
EP3259590A1 EP3259590A1 (en) 2017-12-27
EP3259590A4 true EP3259590A4 (en) 2018-10-17

Family

ID=56689498

Family Applications (1)

Application Number Title Priority Date Filing Date
EP16753186.2A Withdrawn EP3259590A4 (en) 2015-02-20 2016-02-19 Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform

Country Status (5)

Country Link
EP (1) EP3259590A4 (en)
AU (1) AU2016219812A1 (en)
CA (1) CA2976923A1 (en)
HK (1) HK1248806A1 (en)
WO (1) WO2016134310A1 (en)

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20140200166A1 (en) * 2013-01-17 2014-07-17 Edico Genome, Inc. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US20140371109A1 (en) * 2013-01-17 2014-12-18 Edico Genome, Corp. Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002048195A2 (en) * 2000-10-23 2002-06-20 Engeneos, Inc. Engineered stimulus-responsive switches
US9928338B2 (en) * 2011-06-01 2018-03-27 The Board Of Trustees Of The Leland Stanford Junior University Method and system for phasing individual genomes in the context of clinical interpretation
GB2496016B (en) * 2011-09-09 2016-03-16 Univ Leland Stanford Junior Methods for obtaining a sequence
JP5809572B2 (en) * 2012-01-30 2015-11-11 ルネサスエレクトロニクス株式会社 Semiconductor device
US10847248B2 (en) * 2012-08-10 2020-11-24 The Board Of Trustees Of The Leland Stanford Junior University Techniques for determining haplotype by population genotype and sequence data

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20140200166A1 (en) * 2013-01-17 2014-07-17 Edico Genome, Inc. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US20140371109A1 (en) * 2013-01-17 2014-12-18 Edico Genome, Corp. Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
ARPITH C JACOB ET AL: "Preliminary results in accelerating profile HMM search on FPGAs", PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM, 2007. IPDPS 2007. IEEE INTERNATIONAL, IEEE, PI, 20 September 2008 (2008-09-20), pages 1 - 8, XP031175492, ISBN: 978-1-4244-0909-9 *
JUAN FERNANDO EUSSE ET AL: "A Protein Sequence Analysis Hardware Accelerator Based on Divergences", INTERNATIONAL JOURNAL OF RECONFIGURABLE COMPUTING, vol. 2012, 1 January 2012 (2012-01-01), Cairo / New York, pages 1 - 19, XP055503584, ISSN: 1687-7195, DOI: 10.1155/2012/201378 *
OLIVER T ET AL: "Integrating FPGA acceleration into HMMer", PARALLEL COMPUTING, ELSEVIER, AMSTERDAM, NL, vol. 34, no. 11, 1 November 2008 (2008-11-01), pages 681 - 691, XP025610243, ISSN: 0167-8191, [retrieved on 20080920], DOI: 10.1016/J.PARCO.2008.08.003 *
See also references of WO2016134310A1 *

Also Published As

Publication number Publication date
CA2976923A1 (en) 2016-08-25
WO2016134310A1 (en) 2016-08-25
EP3259590A1 (en) 2017-12-27
AU2016219812A1 (en) 2017-08-31
HK1248806A1 (en) 2018-10-19

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Inventor name: RUEHLE, MICHAEL

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Inventor name: MCMILLEN, ROBERT, J.

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Owner name: EDICO GENOME, INC.

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