Figure 1

Shustrings on forward and backward strands. Global and local shortest unique substrings ('shustrings') in the DNA-sequence ACCG. A: The global shustrings are A and G, and have length 1 (black numbers above the sequence). The numbers above the sequence indicate the length of the four local shustrings A, CC, CG and G present on the forward strand. B: In the presence of the reverse strand global as well as local shustrings may change. For some positions at the 3'end of the sequence shustrings may not be defined (here, position 3 and 4 on the forward strand). Notice that the complement of a local shortest unique substring is also unique, however not necessarily a shortest unique substring (for example the pair GT on the reverse strand and AC on the forward strand). The complement of a global shortest unique substring is again a global shortest unique substring (here the two global shustrings A and T).