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Comparative Genometrics


NAR Molecular Biology Database Collection entry number 884
Roten C.-A.H.1, Gamba P.2, Barblan J.-L.1 and Karamata D.1
1DÉpartement de Microbiologie Fondamentale, UniversitÉ de Lausanne, BÂtiment de Biologie - Biophore, Quartier Sorge, CH-1015 Lausanne-Dorigny, Switzerland
2Genometrician's Company S.A., rue du Centre 45, CH-1025 Saint-Sulpice, Switzerland

Database Description

The ever increasing rate at which whole genome sequences are becoming accessible to the scientific community has created an urgent need for tools enabling comparison of chromosomes of different species. We have applied biometric methods to available chromosome sequences and posted the results on our Comparative Genometrics (CG) web site. By genometrics, a term coined by Elston and Wilson [Genet. Epidemiol. (1990), 7, 17-19], we understand a biometric analysis of chromosomes. During the initial phase, our web site displays, for all completely sequenced prokaryotic genomes, three genometric analyses: the DNA walk [Lobry (1999) Microbiology Today, 26, 164-165] and two complementary representations, i.e. the cumulative GC- and TA-skew analyses, capable of identifying, at the level of whole genomes, features inherent to chromosome organization and functioning. It appears that the latter features are taxon-specific. Although primarily focused on prokaryotic chromosomes, the CG web site contains genometric information on paradigm plasmids, phages, viruses and eukaryotic organelles. Relevant data and methods can be readily used by the scientific community for further analyses as well as for tutorial purposes. Our data posted at the CG web site are freely available on the World Wide Web at http://www.unil.ch/comparativegenometrics.

Recent Developments

The whole site was redesigned, update processing has been almost fully automated, thus allowing more frequent updates, generally once a month. Each page now includes taxonomical information on the analyzed chromosome. Completing the basic number of nucleotides, the G+C content is calculated for the whole chromosome. Future analyses will include genometric detection of putative origin and terminus of replication, nucleotide skews on different genomic subsets, residual skews, ORF orientation skews, dinucleotide and codon count and biases.

Acknowledgements

Lionel Guy is presently maintaing and developing the database, under the supervision of Claude-Alain H. Roten. The recent and future developments have been possible thanks to the technical help of Antoine Jover.

References

1. Guy L, Karamata D, Moreillon P, Roten CA. (2005) Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705. BMC Microbiol. 5: 60.
2. Guy L, Roten CA. (2004) Genometric analyses of the organization of circular chromosomes: a universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication. Gene 340: 45-52.


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