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Title: Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences

Abstract

A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

Inventors:
 [1];  [1];  [2];  [3];  [4]
  1. Los Angeles, CA
  2. Sherman Oaks, CA
  3. Santa Monica, CA
  4. Agoura Hills, CA
Issue Date:
Research Org.:
Univ. of California (United States)
OSTI Identifier:
874814
Patent Number(s):
6466874
Application Number:
09/493,497
Assignee:
The Regents of the University of California (Oakland, CA)
Patent Classifications (CPCs):
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
DOE Contract Number:  
FC03-87ER60615
Resource Type:
Patent
Country of Publication:
United States
Language:
English
Subject:
rosetta; stone; method; detecting; protein; function; protein-protein; interactions; genome; sequences; computational; computer; provided; inferring; functional; links; based; observation; pairs; proteins; homologs; organism; fused; single; chain; trans-genome; comparison; reveal; decipher; interaction; compares; genomic; sequence; organisms; create; phylogenetic; profile; indicating; presence; absence; genomes; provides; information; regarding; families; combination; methods; predict; provides information; /702/435/530/

Citation Formats

Eisenberg, David, Marcotte, Edward M, Pellegrini, Matteo, Thompson, Michael J, and Yeates, Todd O. Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences. United States: N. p., 2002. Web.
Eisenberg, David, Marcotte, Edward M, Pellegrini, Matteo, Thompson, Michael J, & Yeates, Todd O. Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences. United States.
Eisenberg, David, Marcotte, Edward M, Pellegrini, Matteo, Thompson, Michael J, and Yeates, Todd O. Tue . "Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences". United States. https://www.osti.gov/servlets/purl/874814.
@article{osti_874814,
title = {Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences},
author = {Eisenberg, David and Marcotte, Edward M and Pellegrini, Matteo and Thompson, Michael J and Yeates, Todd O},
abstractNote = {A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2002},
month = {1}
}

Works referenced in this record:

Microbial Genescapes: A Prokaryotic View of the Yeast Genome
journal, January 1998


A novel genetic system to detect protein–protein interactions
journal, July 1989


Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli
journal, March 1996


A combined algorithm for genome-wide prediction of protein function
journal, November 1999


Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
journal, April 1999


Protein interaction maps for complete genomes based on gene fusion events
journal, November 1999


Constructing Multigenome Views of Whole Microbial Genomes
journal, January 1998


EcoCyc: Encyclopedia of Escherichia coli genes and metabolism
journal, January 1998


A Genomic Perspective on Protein Families
journal, October 1997


The ProDom database of protein domain families
journal, January 1998


The Complete Genome Sequence of Escherichia coli K-12
journal, September 1997


Cluster analysis and display of genome-wide expression patterns
journal, December 1998


Predicting function: from genes to genomes and back 1 1Edited by P. E. Wright
journal, November 1998