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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:
; ; ; ;
Publication Date:
Research Org.:
The Regents of the University of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1174971
Patent Number(s):
6,772,069
Application Number:
09/493,401
Assignee:
University Of California, The Regents Of OSTI
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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