WO2004059556A3 - Verfaren und vorrichtung zum optimieren einer nucleotidsequenz zur expression eines proteins - Google Patents

Verfaren und vorrichtung zum optimieren einer nucleotidsequenz zur expression eines proteins Download PDF

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Publication number
WO2004059556A3
WO2004059556A3 PCT/EP2003/014850 EP0314850W WO2004059556A3 WO 2004059556 A3 WO2004059556 A3 WO 2004059556A3 EP 0314850 W EP0314850 W EP 0314850W WO 2004059556 A3 WO2004059556 A3 WO 2004059556A3
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WO
WIPO (PCT)
Prior art keywords
nucleotide sequence
protein
determined
codons
optimizing
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Application number
PCT/EP2003/014850
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English (en)
French (fr)
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WO2004059556A2 (de
Inventor
David Raab
Marcus Graf
Frank Notka
Ralf Wagner
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Geneart Gmbh
David Raab
Marcus Graf
Frank Notka
Ralf Wagner
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First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=32519349&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2004059556(A3) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority to JP2004563202A priority Critical patent/JP4510640B2/ja
Priority to EP10012880.0A priority patent/EP2363821B1/de
Priority to AU2003294953A priority patent/AU2003294953B2/en
Priority to CA002511503A priority patent/CA2511503A1/en
Priority to DK03785937.8T priority patent/DK1584058T3/en
Application filed by Geneart Gmbh, David Raab, Marcus Graf, Frank Notka, Ralf Wagner filed Critical Geneart Gmbh
Priority to US10/539,208 priority patent/US8224578B2/en
Priority to EP03785937.8A priority patent/EP1584058B1/de
Publication of WO2004059556A2 publication Critical patent/WO2004059556A2/de
Publication of WO2004059556A3 publication Critical patent/WO2004059556A3/de
Priority to US13/524,943 priority patent/US20130123483A1/en
Priority to US14/034,449 priority patent/US20140228558A1/en
Priority to US15/067,079 priority patent/US20160259885A1/en

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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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/43504—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from invertebrates
    • C07K14/43595—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from invertebrates from coelenteratae, e.g. medusae
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/52—Cytokines; Lymphokines; Interferons
    • C07K14/53—Colony-stimulating factor [CSF]
    • C07K14/535—Granulocyte CSF; Granulocyte-macrophage CSF
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/52—Cytokines; Lymphokines; Interferons
    • C07K14/54—Interleukins [IL]
    • C07K14/5443—IL-15
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/50—Mutagenesis
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • 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

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Medical Informatics (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Organic Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Biochemistry (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Zoology (AREA)
  • Toxicology (AREA)
  • Immunology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

Die Erfindung betrifft ein Verfahren zum Optimieren einer Nucleotidsequenz zur Expression eines Proteins auf der Grundlage der Aminosäurensequenz des Proteins, bei welchem für einen bestimmten Bereich eine Testsequenz mit m Optimierungspositionen festgelegt wird, auf denen die Codonbesetzung variiert wird, wobei mittels einer Gütefunktion die optimale Codonbesetzung auf diesen Optimierungspositionen ermittelt wird und ein oder mehrere Codons dieser optimalen Besetzung als Codons der optimierten Nucleotidsequenz festgelegt werden. Diese Schritte werden iteriert, wobei bei nachfolgenden Iterationsschritten die in vorangehenden Schritten festgelegten Codons der optimierten Nucleotidsequenz unverändert bleiben. Die Erfindung betrifft weiterhin eine Vorrichtung zur Durchführung dieses Verfahrens.
PCT/EP2003/014850 2002-12-23 2003-12-23 Verfaren und vorrichtung zum optimieren einer nucleotidsequenz zur expression eines proteins WO2004059556A2 (de)

Priority Applications (10)

Application Number Priority Date Filing Date Title
EP03785937.8A EP1584058B1 (de) 2002-12-23 2003-12-23 Verfahren und vorrichtung zum optimieren einer nucleotidsequenz zur expression eines proteins
EP10012880.0A EP2363821B1 (de) 2002-12-23 2003-12-23 Verfahren und Vorrichtung zum Optimieren einer Nucleotidsequenz zur Expression eines Proteins
AU2003294953A AU2003294953B2 (en) 2002-12-23 2003-12-23 Method and device for optimizing a nucleotide sequence for the purpose of expression of a protein
CA002511503A CA2511503A1 (en) 2002-12-23 2003-12-23 Method and device for optimizing a nucleotide sequence for the purpose of expression of a protein
DK03785937.8T DK1584058T3 (en) 2002-12-23 2003-12-23 PROCEDURE AND APPARATUS FOR OPTIMIZING A NUCLEOTIDE SEQUENCE FOR EXPRESSION OF A PROTEIN
JP2004563202A JP4510640B2 (ja) 2002-12-23 2003-12-23 タンパク質の発現を目的としてヌクレオチド配列を最適化する方法及び装置
US10/539,208 US8224578B2 (en) 2002-12-23 2003-12-23 Method and device for optimizing a nucleotide sequence for the purpose of expression of a protein
US13/524,943 US20130123483A1 (en) 2002-12-23 2012-06-15 Method and device for optimizing a nucelotide sequence for the purpose of expression in a protein
US14/034,449 US20140228558A1 (en) 2002-12-23 2013-09-23 Method and device for optimizing a nucelotide sequence for the purpose of expression in a protein
US15/067,079 US20160259885A1 (en) 2002-12-23 2016-03-10 Method and device for optimizing a nucelotide sequence for the purpose of expression in a protein

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
DE10260805.9 2002-12-23
DE10260805A DE10260805A1 (de) 2002-12-23 2002-12-23 Verfahren und Vorrichtung zum Optimieren einer Nucleotidsequenz zur Expression eines Proteins

Related Child Applications (2)

Application Number Title Priority Date Filing Date
US10/539,208 A-371-Of-International US8224578B2 (en) 2002-12-23 2003-12-23 Method and device for optimizing a nucleotide sequence for the purpose of expression of a protein
US13/524,943 Continuation US20130123483A1 (en) 2002-12-23 2012-06-15 Method and device for optimizing a nucelotide sequence for the purpose of expression in a protein

Publications (2)

Publication Number Publication Date
WO2004059556A2 WO2004059556A2 (de) 2004-07-15
WO2004059556A3 true WO2004059556A3 (de) 2005-12-01

Family

ID=32519349

Family Applications (1)

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PCT/EP2003/014850 WO2004059556A2 (de) 2002-12-23 2003-12-23 Verfaren und vorrichtung zum optimieren einer nucleotidsequenz zur expression eines proteins

Country Status (8)

Country Link
US (4) US8224578B2 (de)
EP (2) EP2363821B1 (de)
JP (1) JP4510640B2 (de)
AU (1) AU2003294953B2 (de)
CA (1) CA2511503A1 (de)
DE (1) DE10260805A1 (de)
DK (1) DK1584058T3 (de)
WO (1) WO2004059556A2 (de)

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