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:

Pellegrini, Matteo; Marcotte, Edward M.; Thompson, Michael J.; Eisenberg, David; Grothe, Robert; Yeates, Todd O.

Issue Date:

Tue May 13 00:00:00 EDT 2003

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

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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

G16B10/00 - ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
G16B20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
G16B20/30 - Detection of binding sites or motifs
G16B20/50 - Mutagenesis
G16B30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids

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DOE Contract Number:  

FC03-87ER60615

Resource Type:

Patent

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES