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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}
}

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