Research
Genomic DNA k-mer spectra: models and modalities
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* Corresponding author: Benny Chor benny@cs.tau.ac.il
1 School of Computer Science, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040, Israel
2 School of Physics and Astronomy, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040, Israel
3 European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
Genome Biology 2009, 10:R108 doi:10.1186/gb-2009-10-10-r108
Published: 8 October 2009Additional files
Additional data file 1:
On the top are 9-mer spectra of human chromosomes (left to right) 1, 6, 20. At the bottom are 11-mer spectra of human chromosomes (left to right) 1, 6, 20. All six spectra are multimodal.
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Additional data file 2:
Whole genome spectra of human (top) and opossum (bottom); 9-mers (left) and 11-mers (right). All four spectra are multimodal.
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Additional data file 3:
From top-left: Escherichia coli, Aeropyrum pernix, zebrafish (Danio rerio), pufferfish (Tetraodon nigroviridis), Arabidopsis thaliana, bee (Apis mellifera), nematode (Caenorhabditis elegans), yeast (Saccharomyces cerevisiae), and sea squirt (Ciona savignyi). All spectra are unimodal.
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Additional data file 4:
Chicken (k = 10), platypus (Ornithorhynchus anatinus, an egg laying mammal; k = 10), frog (k = 11), and lizard (k = 11). All four k-mer spectra are multimodal.
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Additional data file 5:
Each plot is partitioned according to 8-mers that contain the CpG dimer (colored green), and those that do not (colored blue). The green ones comprise the left-most part in the multimodal spectra for (a) human, and (b) chicken. In the two other, non-tetrapodal species, (c) C. elegans (nematode), and (d) pufferfish, there is no such effect.
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Additional data file 6:
Whole genome (k = 10), all introns (k = 10), all 3' UTRs (k = 10), all exons (k = 9), all 5' UTRs (k = 8), all 600 base long promotors (k = 6), all 1,000 base long promotors (k = 7), all 5,000 base long promotors (k = 7).
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Additional data file 7:
Additional information includes taxonomical classification, usable length, percentage C+G content, CpG suppression (measured by ρCG) and whether the k-mer spectrum is observed to have unimodal or multimodal behavior. It also specifies web sites from which sequences were downloaded [22-27], and where different functional genomic regions were downloaded from [28-30].
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