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Open Access Research article

Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics

Artem Cherkasov1*, Shannan J Ho Sui2, Robert C Brunham13 and Steven JM Jones4

Author Affiliations

1 Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada

2 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada

3 University of British Columbia Center for Disease Control, Vancouver, British Columbia, Canada

4 Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada

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BMC Bioinformatics 2004, 5:101  doi:10.1186/1471-2105-5-101

Published: 26 July 2004

Abstract

Background

We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, maintainability and safety work to model time-to-failure of mechanical devices, mechanisms, building constructions and equipment.

Results

We have found that the Weibull function describes protein fold distribution within and among genomes more accurately than conventional power functions which have been used in a number of structural genomic studies reported to date.

It has also been found that the Weibull reliability parameter β for protein fold distributions varies between genomes and may reflect differences in rates of gene duplication in evolutionary history of organisms.

Conclusions

The results of this work demonstrate that reliability analysis can provide useful insights and testable predictions in the fields of comparative and structural genomics.