Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes

Table 4 The definitions of color function.

α < 0	Color(α)	α < 0	Color(α)	α > 0	Color(α)	α > 0	Color(α)
> -26.0λ	0,0,80	-3.5λ	0,0,228	0.0λ	0,0,0	4.5λ	0,201,0
-26.0λ	0,0,80	-1.5λ	0,0,255	0.01λ	190,85,0	7.5λ	0,174,0
-21.0λ	0,0,97	-1.0λ	85,0,255	0.08λ	255,170,0	9.0λ	0,145,0
-14.5λ	0,0,113	-0.5λ	170,0,255	0.2λ	255,255,0	12.0λ	0,129,0
-12.0λ	0,0,129	-0.2λ	255,0,255	0.5λ	170,255,0	14.5λ	0,113,0
-9.0λ	0,0,145	-0.08λ	255,0,170	1.0λ	85,255,0	21.0λ	0,97,0
-7.5λ	0,0,174	-0.01λ	190,0,85	1.5λ	0,255,0	26.0λ	0,80,0
-4.5λ	0,0,201	-0.0λ	0,0,0	3.5λ	0.228,0	> 26.0λ	0,80,0

The color function Color(α) is defined as this table, where α is the AT or CG skew and λ is |(A - T)/(A + T)| + |(C - G)/(C + G))| (equation 3) for whole genome. Since the λ is different for genomes, the color function depends on the value of λ. Corresponding color scale is in Figure 4. Color(α) maps the AT or CG skew α to a RGB color. For example if the skew value is -3.5λ (top of the third vertical row) the color is (0, 0, 228). The λ may be different for different chromosomes.

ISSN: 2730-7182