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Open Access Research article

Structural characterization of genomes by large scale sequence-structure threading

Artem Cherkasov12* and Steven JM Jones1

Author Affiliations

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

2 Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada

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BMC Bioinformatics 2004, 5:37  doi:10.1186/1471-2105-5-37

Published: 3 April 2004

Abstract

Background

Using sequence-structure threading we have conducted structural characterization of complete proteomes of 37 archaeal, bacterial and eukaryotic organisms (including worm, fly, mouse and human) totaling 167,888 genes.

Results

The reported data represent first rather general evaluation of performance of full sequence-structure threading on multiple genomes providing opportunity to evaluate its general applicability for large scale studies.

According to the estimated results the sequence-structure threading has assigned protein folds to more then 60% of eukaryotic, 68% of archaeal and 70% of bacterial proteomes.

The repertoires of protein classes, architectures, topologies and homologous superfamilies (according to the CATH 2.4 classification) have been established for distant organisms and superkingdoms. It has been found that the average abundance of CATH classes decreases from "alpha and beta" to "mainly beta", followed by "mainly alpha" and "few secondary structures".

3-Layer (aba) Sandwich has been characterized as the most abundant protein architecture and Rossman fold as the most common topology.

Conclusion

The analysis of genomic occurrences of CATH 2.4 protein homologous superfamilies and topologies has revealed the power-law character of their distributions. The corresponding double logarithmic "frequency – genomic occurrence" dependences characteristic of scale-free systems have been established for individual organisms and for three superkingdoms.

Supplementary materials to this works are available at [1].