WO2003058205A3 - Methods of identifying putative effector proteins - Google Patents

Methods of identifying putative effector proteins Download PDF

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Publication number
WO2003058205A3
WO2003058205A3 PCT/US2003/000911 US0300911W WO03058205A3 WO 2003058205 A3 WO2003058205 A3 WO 2003058205A3 US 0300911 W US0300911 W US 0300911W WO 03058205 A3 WO03058205 A3 WO 03058205A3
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WO
WIPO (PCT)
Prior art keywords
amino acid
acid sequence
rules
methods
effector proteins
Prior art date
Application number
PCT/US2003/000911
Other languages
French (fr)
Other versions
WO2003058205A2 (en
Inventor
Alan Collmer
James Alfano
David Schneider
Lisa Schechter
Original Assignee
Cornell Res Foundation Inc
Univ Nebraska
Us Agriculture
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 Cornell Res Foundation Inc, Univ Nebraska, Us Agriculture filed Critical Cornell Res Foundation Inc
Priority to AU2003226441A priority Critical patent/AU2003226441A1/en
Publication of WO2003058205A2 publication Critical patent/WO2003058205A2/en
Publication of WO2003058205A3 publication Critical patent/WO2003058205A3/en

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Evolutionary Computation (AREA)
  • Bioethics (AREA)
  • Genetics & Genomics (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Urology & Nephrology (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Biomedical Technology (AREA)
  • Artificial Intelligence (AREA)
  • Hematology (AREA)
  • Immunology (AREA)
  • Cell Biology (AREA)
  • Microbiology (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Biochemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

A system and method for identifying putative effector proteins that includes providing a predicted amino acid sequence and determining whether the predicted amino acid sequence satisfies one or more rules from a set of rules that applies to known effector protein amino acid sequences, wherein satisfaction of the one or more rules indicates that the predicted amino acid sequence is likely an effector protein. A computer readable medium is also disclosed herein as having stored thereon instructions which, when executed by a processor, cause the processor to perform such a determination.
PCT/US2003/000911 2002-01-11 2003-01-13 Methods of identifying putative effector proteins WO2003058205A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2003226441A AU2003226441A1 (en) 2002-01-11 2003-01-13 Methods of identifying putative effector proteins

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US34806102P 2002-01-11 2002-01-11
US60/348,061 2002-01-11

Publications (2)

Publication Number Publication Date
WO2003058205A2 WO2003058205A2 (en) 2003-07-17
WO2003058205A3 true WO2003058205A3 (en) 2003-12-18

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2003/000911 WO2003058205A2 (en) 2002-01-11 2003-01-13 Methods of identifying putative effector proteins

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AU (1) AU2003226441A1 (en)
WO (1) WO2003058205A2 (en)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN104899478B (en) * 2015-07-03 2018-03-16 景德镇陶瓷大学 A kind of solution method of the protein training set imbalance problem of new blending inheritance information
CN110400604B (en) * 2019-06-28 2021-10-08 中国科学院计算技术研究所 Method and system for analyzing codon usage pattern of multiple species in Rutaceae
CN116092575A (en) * 2023-02-03 2023-05-09 中国科学院地理科学与资源研究所 G DNA structure discrimination method based on GMNS rule

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6225085B1 (en) * 1998-04-21 2001-05-01 Millennium Biotherapeutics, Inc. LRSG protein and nucleic acid molecules and uses therefor
US6309651B1 (en) * 1998-11-25 2001-10-30 Mcw Research Foundation Method of and compositions for immunization with the pseudomonas V antigen

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6225085B1 (en) * 1998-04-21 2001-05-01 Millennium Biotherapeutics, Inc. LRSG protein and nucleic acid molecules and uses therefor
US6309651B1 (en) * 1998-11-25 2001-10-30 Mcw Research Foundation Method of and compositions for immunization with the pseudomonas V antigen

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
ANDERSON ET AL.: "A mRNA signal for the type III secretion of Yop proteins by Yersinia enterocolitica", SCIENCE, vol. 278, 7 November 1997 (1997-11-07), pages 1140 - 1143, XP002921388 *
ANDERSON ET AL.: "Reciprocal secretion of proteins by the bacterial type III machine of plant and animal pathogens suggests universal recognition of mRNA targeting signals", PROC. NATL. ACAD. SCI. USA, vol. 96, no. 22, 26 October 1999 (1999-10-26), pages 12839 - 12843, XP002968580 *
CORNELIS ET AL.: "Assembly and function of type III secretory systems", ANNU. REV. MICROBIOL., vol. 54, 2000, pages 735 - 774, XP002968578 *
MIAO ET AL.: "A conserved amino acid sequence direction intracellular type III secretion by Salmonella Typhimurium", PROC. NATL. ACAD. SCI. USA, vol. 97, no. 13, 20 June 2000 (2000-06-20), pages 7539 - 7544, XP002965016 *
MUDGETT ET AL.: "Molecular signals required for type III secretion and translocation of the xanthomonas campestris AvrBs2 protein to pepper plants", PROC. NATL. ACAD. SCI. USA, vol. 97, no. 21, 21 November 2000 (2000-11-21), pages 13324 - 13329, XP002968579 *
SORY ET AL.: "Identification of the YopE and the YopH domains required for secretion and internalization into the cytosol of macrophages, using the cyaA gene fusion approach", PROC. NATL. ACAD. SCI. USA, vol. 92, December 1995 (1995-12-01), pages 11998 - 12002, XP002921387 *

Also Published As

Publication number Publication date
WO2003058205A2 (en) 2003-07-17
AU2003226441A1 (en) 2003-07-24
AU2003226441A8 (en) 2003-07-24

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