Resolution:
## Figure 2.
Searches for different types of patterns. Searching for sequence patterns based on (a) base composition, (b) exact matches,
and (c) degenerate base patterns. (d) A simplified example of the bit masking approach
for 3-base patterns and 12-base windows. Calculate the integer X1 for the string S1
as the sum of 2^{bit-pos}, where bit-pos refers to bit positions (0 to 23) for each bit set to 1. Each bitvector
is followed by its corresponding decimal value (in parentheses). Similarly, calculate
integer values for the overlapping string S2 and for the upper (U1 and U2) and lower
(L1 and L2) bounds for two search patterns (TAT and ATC). The bit patterns for windows
S1 and S2 are shown using the notation for bases in Figure 1a. The bit patterns for
the search patterns, TAT and ATC, are indicated by an underline, and the remaining
positions are masked with a value of either 0 or 1 for the lower and upper integer
limits (as shown for S1), respectively. X1 is between L1 and U1, but not between L2
and U2. Similarly, X2 is between L2 and U2, but not between L1 and U1. This example
demonstrates that S1 begins with TAT but not ATC, and S2 begins with ATC but not TAT.
Hamady |