How to find simple and accurate rules for viral protease cleavage specificities

BMC Bioinformatics

Table 10 Mixing of HIV-1 rules.

HIV..	..A1	..B1	..C1	..D1	..E1	..A2	..B2	..C2	..D2	..E2
HIVA1	4.56%	1.90%	0.36%	0.27%	1.60%	3.45%	0.43%	0.41%	0.43%	0.29%
HIVB1		4.29%	0.31%	0.19%	0.93%	0.73%	0.53%	0.31%	0.16%	0.28%
HIVC1			3.23%	0.14%	0.12%	0.29%	0.24%	0.25%	0.25%	0.26%
HIVD1				2.05%	0.17%	0.28%	0.12%	0.31%	0.20%	0.22%
HIVE1					3.50%	1.58%	0.20%	0.17%	0.22%	0.12%
HIVA2						4.97%	0.54%	0.53%	0.67%	0.32%
HIVB2							2.56%	0.62%	0.22%	0.63%
HIVC2								1.86%	0.53%	0.55%
HIVD2									1.53%	0.41%
HIVE2										2.70%

There are 20⁸ possible octamers.
The fractions of these octamers that match to each OSRE HIV-1 rule, and to more than one rule, are shown here. The diagonal elements in the table show the fraction of the possible octamers that match one rule. The off-diagonal elements in the table show what fraction of the octamers that match both rules.

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