• Correlizer

    by Published on 08-23-11 06:07 PM  Number of Views: 831 






    Description: Genomes are fantastic keepers of genetic information and are the outcome of evolutionary replication, mutation and selection. Genomes organize functions from the cellular level, via the organismic level, up to the complex basis of mind. In human cells the genetic information controlling most processes from the cellular level, over embryogenesis to cognitive ability, manifests in a diploid set of 23 DNA molecules (chromosomes), combined they consist of ~3x10^9 base pairs (bp) stored in ~2.80 GB of data. This whole genome, whose added molecular length totals ~2m, is kept in comparably small cell nuclei with typical diameters of ~10 Ám or volumes of 500 Ám^3. The sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional architectural organization of genomes is still a largely unresolved problem.
    http://svahesrv2.bioquant.uni-heidel...cleus-ACGT.jpg
    Correlizer has been set up to unravel these mysteries, and we found long-range power-law correlations on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 x 10^6 to 3.0 x 10^7 bp. Varying from Archaea, Bacteria, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens. The local correlation coefficients show a species-specific multi-scaling behavior: close to random correlations on the scale of a few base pairs, a first maximum from 40 to 3,400 bp (for Arabidopsis thaliana and Drosophila melanogaster divided in two submaxima), and often a region of one or more second maxima from 10^5 to 3 x 10^5 bp. Within this multi-scaling behavior, an additional fine-structure is present and attributable to codon usage in all except the human sequences, where it is related to nucleosomal binding.


    Institution: The applications come from the Group Biophysical Genomics, Dept. Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands, and distributed threw the Erasmus Grid Office, Erasmus Medical Center, Rotterdam, The Netherlands.
    This server is hosted by the Group Genome Organization & Function, BioQuant Center/German Cancer Research Center, Heidelberg, Germany.


    Home Page:http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/


    Project Status: Active.


    Client Programs: The project supports the following Applications:
    Microsoft Windows (98 or later) running on an Intel x86-compatible CPU
    Linux running on an Intel x86-compatible CPU
    Linux running on an AMD x86_64 or Intel EM64T CPU
    Mac OS 10.4 or later running on Intel
    Intel 64-bit Mac OS 10.5 or later


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