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Title: Determining protein function and interaction from genome analysis

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:
; ; ; ;
Issue Date:
Research Org.:
Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1174971
Patent Number(s):
6772069
Application Number:
09/493,401
Assignee:
University Of California, The Regents Of
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:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Eisenberg, David, Marcotte, Edward M., Thompson, Michael J., Pellegrini, Matteo, and Yeates, Todd O. Determining protein function and interaction from genome analysis. United States: N. p., 2004. Web.
Eisenberg, David, Marcotte, Edward M., Thompson, Michael J., Pellegrini, Matteo, & Yeates, Todd O. Determining protein function and interaction from genome analysis. United States.
Eisenberg, David, Marcotte, Edward M., Thompson, Michael J., Pellegrini, Matteo, and Yeates, Todd O. Tue . "Determining protein function and interaction from genome analysis". United States. https://www.osti.gov/servlets/purl/1174971.
@article{osti_1174971,
title = {Determining protein function and interaction from genome analysis},
author = {Eisenberg, David and Marcotte, Edward M. and Thompson, Michael J. and Pellegrini, Matteo 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 = {2004},
month = {8}
}

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Works referenced in this record:

Conservation of gene order: a fingerprint of proteins that physically interact
journal, September 1998


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


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


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


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


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


A Genomic Perspective on Protein Families
journal, October 1997


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


The ProDom database of protein domain families
journal, January 1998


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


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


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