have the potential to help in interpretation of genetic association studies results, when associations are found with SNPs mapping to ‘‘gene deserts’’ [24]. Methods For this overview of dinucleotide periodicities in eukaryotes, we selected sequences from a number of well characterized model organisms, supplemented by others in order to be more representative. Besides, we only included genomes, where a documented assembly into chromosomes was available. Genomic sequences of Caenorhabditis elegans (ce6, genome.ucsc.edu), Arabi- dopsis thaliana (build of 20 Dec 2007, ftp.arabidopsis.org), Anopheles gambiae (AgamP3, agambiae.vectorbase.org), Apis mellifera (apiMel4, ftp.hgsc.bcm.tmc.edu), Saccharomyces cerevisiae (sacCer1, genome. ucsc.edu), Gallus gallus (galGal3, genome.ucsc.edu), Mus musculus (mm9, genome.ucsc.edu), Homo sapiens (hg18, genome.ucsc.edu), Candida albicans (Ca21, www.candidagenome.org), Chlamydomonas reinhardtii (Chlre4, genomes.jpg-psf.org), Danio rerio (danRer5, genome.ucsc.edu), Dictyostelium discoideum (Ver. May 2009, dictybase. org) and Drosophila melanogaster (dm3, genome.ucsc.org) were downloaded from the respective server. Dinucleotide positions in sequences (grouped into chromosomes) were determined by pattern search and recorded in a file. From these files, for every dinucleotide the distances to the next identical dinucleotides in a downstream interval of 150 bases were calculated (positional autocorrelation analysis) and recorded. Then, the start point for the next interval was shifted to the next identical dinucleotide. Calculated distances were summed over the chromosomes (C. elegans chrI to chrV and chrX, A. thaliana chr1 to chr5, A. gambiae chr2L, chr2R, chr3L, chr3R, A. mellifera group1 to group16, S. cerevisiae chr1 to chr16, G. gallus chr1 to chr28, M. musculus chr1 to chr19, H. sapiens chr1 to References 1. Trifonov EN, Sussman JL (1980) The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc Natl Acad Sci U S A 77: 3816–3820. 2. Mengeritsky G, Trifonov EN (1983) Nucleotide sequence-directed mapping of the nucleosomes. Nucl Acids Res 11: 3833–3851. 3. Bolshoy A (1995) CC dinucleotides contribute to the bending of DNA in chromatin. Nature Struct Biol 2: 446–448. 4. 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Modelling of biomolecular structures and mechanisms. Dordrecht: Kluwer. pp 473–479. 11. Cohanim AB, Kashi Y, Trifonov EN (2006) Three sequence rules for chromatin. J Biomol Str Dyn 23: 559–566. 12. Trifonov EN (1980) Sequence-dependent deformational anisotropy of chromatin DNA. Nucl Acids Res 8: 4041–4053. 13. Davey C, Pennings S, Allan J (1997) CpG methylation remodels chromatin structure in vitro. J Mol Biol 267: 276–288. Nucleosome Positioning chr22, C. albicans chr1 to chr5, C. reinhardtii Chr1 to Chr17, D. rerio Chr1 to Chr25, D. dictyostelium Chr1 to chr6 and D. melanogaster chr2L, chr2R, chr3L, chr3R and chr4). Counts for distances were arranged in histograms and smoothened by averaging over 3 bases. Statistical significance of the data has been estimated as in [1] by relating excess values in the observed periodical peaks to respective background scores. In case of the weakest oscillations found, for S. cerevisiae (CA, CC, AG and TA, see Fig. 2), the cumulative effects of the excess values amount, respectively, to 3.0, 2.9, 2.9 and 3.9 STD. This is in full agreement with the estimates first made in [6]. All 208 plots were evaluated for visibility of a 10.4 bp periodicity. When visible, a ‘‘+’’ was entered into Table 1, otherwise a ‘‘2’’. The data in the rows and columns of Table 1 are sorted by the size of the repertoires of periodic dinucleotides. Human sequences have been analysed both as unfiltered and after filtering out major repeats, Alu repeats in particular, by using the sequence data available under the label ‘‘masked’’ (hg18, file chromFaMasked.zip, genome.ucsc.edu). The data from the filtered sequence was considered for the H. sapiens entry in Table 1. Mitochondrial and unmapped sequences were not taken for the analyses. 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