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Title: Assigning protein functions by comparative genome analysis protein phylogenetic profiles

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:
1174330
Patent Number(s):
6564151
Application Number:
09/493,498
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:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Pellegrini, Matteo, Marcotte, Edward M., Thompson, Michael J., Eisenberg, David, Grothe, Robert, and Yeates, Todd O. Assigning protein functions by comparative genome analysis protein phylogenetic profiles. United States: N. p., 2003. Web.
Pellegrini, Matteo, Marcotte, Edward M., Thompson, Michael J., Eisenberg, David, Grothe, Robert, & Yeates, Todd O. Assigning protein functions by comparative genome analysis protein phylogenetic profiles. United States.
Pellegrini, Matteo, Marcotte, Edward M., Thompson, Michael J., Eisenberg, David, Grothe, Robert, and Yeates, Todd O. Tue . "Assigning protein functions by comparative genome analysis protein phylogenetic profiles". United States. https://www.osti.gov/servlets/purl/1174330.
@article{osti_1174330,
title = {Assigning protein functions by comparative genome analysis protein phylogenetic profiles},
author = {Pellegrini, Matteo and Marcotte, Edward M. and Thompson, Michael J. and Eisenberg, David and Grothe, Robert 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 = {2003},
month = {5}
}

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Works referenced in this record:

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


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


Measuring genome evolution
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A combined algorithm for genome-wide prediction of protein function
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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
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A Genomic Perspective on Protein Families
journal, October 1997