text: The sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes is still a largely unresolved problem. Long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5 x 106 to 3.0 x 107 bp from Archaea, Bacteria, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, and Homo sapiens. The local correlation coefficients show a species-specific multi-scaling behaviour: 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 105 to 3 x 105 bp. Within this multi-scaling behaviour, an additional fine-structure is present and attributable to codon usage in all except the human sequences, where it is related to nucleosomal binding. Computer-generated random sequences assuming a block organization of genomes, the codon usage, and nucleosomal binding explain these results. Mutation by sequence reshuffling destroyed all correlations. Thus, the stability of correlations seems to be evolutionarily tightly controlled and connected to the spatial genome organization, especially on large scales. In summary, genomes show a complex sequential organization related closely to their three-dimensional organization.
  The application comes from the Group Biophysical Genomics, Dept. Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands, and distibuted threw the Erasmus Grid Office, Erasmus Medical Center, Rotterdam, The Netherlands.
  The server is hosted by the Group Genome Organization & Function, BioQuant Center/German Cancer Research Center, Heidelberg, Germany.
  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
  Connecting to Project
  The projects Home Page and URL for joining the project ist: http://svahesrv2.bioquant.uni-heidelberg.de/correlizer/