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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]