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Table 1 Some uses of the oligonucleotide profiling strategy. Typical values for the word size (k) and range parameter (R) for analyses involving eukaryotic chromosomes are detailed. If small eukaryotic chromosomes or bacterial genomes are analyzed, the most convenient k and R values may be smaller. When two or more sources are used, results are obtained independently and then compared. Some examples are shown in detail in the supplementary information (Supplementary figures 1 – 5).

From: Fast comparison of DNA sequences by oligonucleotide profiling

Type of analysis Source Target Typical word sizes (K) Typical ranges (R) Examples
Oligonucleotide, microsatellite quantification, chaos game representation Any DNA sequence Same as Source 1–8 1 See Refs. [2, 21]
Degree of conservation within a repetitive sequence Chromosome Repetitive sequence 10–14 1 Suppl. Figs. 1A, 2
Variations in repetitive content Two or more chromosomes Repetitive sequence 10–14 1 Suppl. Fig. 3
Sequence localization Short sequence Chromosome 1–14 103-106 Suppl. Figs. 1B, 4
Degree of sequence conservation or changes in sequence complexity among chromosomes Two or more chromosomes One of the chromosomes 12–14 1–105 Suppl. Fig. 5
Detection of singular sequences Two chromosomes One of the chromosomes 12–14 1 See Ref. [19]