Genome Diversity Center

at the Institute of Evolution, University of Haifa

(Since August 2000)
Head: Edward N. Trifonov




Are genomes built of units?


A conspicuous uniformity of protein fold sizes, of DNA rings, of dinucleosome units, et al.
suggests a stage in evolution when the genes and their products represented the uniform genome units.
The units are of about 400 base pairs (120-150 amino acids), somewhat different for prokaryotes and eukaryotes.

Relevant references:

Cohanim, A. B., Trifonov, E. N., Kashi, Y.,
Specific selection pressure on the third codon positions: contribution to 10 - 11 base periodicity in prokaryotic genomes.
J. Molec. Evol. 63, 393-400 (2006)

Hosid, S., Trifonov, E. N., Bolshoy, A.,
Sequence periodicity of Escherichia coli genome is concentrated in intergenic regions.
BMC Molecular Biology 5:14 (2004).
http://www.biomedcentral.com/bmcmolbiol/

Makhoul, C. H., Trifonov, E. N.,
Distribution of rare triplets along mRNA and their relation to protein folding,
J Biomolec Str Dyn 20, 413-420 (2002)

Trifonov, E. N., Segmented genome: elementary units of genome structure,
Russian J. of Genetics 38, 659-663 (2002)

Kolker, E., Tjaden, B. C., Hubley, R., Trifonov, E. N., Siegel, A. F.,
Spectral analysis of distributions: finding periodic components in eukaryotic enzyme length data,
OMICS: A Journal of Integrative Biology 6, 123-130 (2002)
http://www.liebertpub.com/OMI/default1.asp

Trifonov, E. N., Denisov, D. A., Makhoul, C., Interacting sequence patterns.
Math. Modelling and Sci. Computing 9, 24-29 (1998)

Trifonov, E. N., How basics of protein evolution could help the gene finding.
Proccedings of the First International Conference on Bioinformatics of Genome Regulation and Structure
BGRS'98, Novosibirsk - Altai Mountains, August 24-31, 1998,
ICG, Novosibirsk, 1998, v.2. Bioinformatics of Genome Structure, pp. 266-268

Trifonov, E. N.,
Segmented structure of mobile and separate DNA and RNA elements as suggested by their size distributions.
J. Biomolec. Str. and Dynamics 14, 449-457 (1997)

Kolker, E., Trifonov, E. N., Segments, folds and overall protein structure.
In: "Biological Structure and Dynamics", (Eds. R. H. Sarma and M. H. Sarma), Adenine Press, New York, 1996, pp. 257-266

Kolker, E., Trifonov, E. N., Sequence sizes of eukaryotic enzymes.
In: "Pacific Symposium on Biocomputing'96", (Eds. L. Hunter and T. E. Klein), World Scientific, London, 1995, pp. 461-471

Kolker, E., Trifonov, E. N., Sequence markers of segmented protein structure.
In: "Modelling of biomolecular structures and mechanisms", (Eds. A. Pullman, J. Jortner and B. Pullman),
Kluwer Academic Publishers, Dordrecht, 1995, pp. 461-471

Trifonov, E. N., Hidden segmentation of protein sequences: structural connection with DNA.
As above, pp. 473-479

Trifonov, E. N.,
Segmented structure of protein sequences and early evolution of genome by combinatorial fusion of DNA elements.
J. Molec. Evol. 40, 337-342 (1995)

Kolker, E., Trifonov, E. N., Periodic recurrence of methionines: Fossil of gene fusion?
Proc. Natl. Acad. Sci. USA 92, 557-560 (1995)

Trifonov, E. N., On the recombinational origin of protein-sequence-subunit structure.
J. Molec. Evol. 38, 543-546 (1994)

Berman, A. L., Kolker, E, Trifonov, E. N., Underlying order in protein sequence organization.
Proc. Natl. Acad. Sci. USA 91, 4044-4047 (1994)