Figure 1.

MEM refinement and extension process

The plot represents four sub-procedures in the process: removing MEMs (in black) whose coordinates on a representative sequence (or query sequence; in blue) are completely included in a larger MEM (in red) (A) or in two neighboring MEMs (in red) (B), trimming the remaining MEMs (in red, e.g., MEM1 in sub-procedure C) of a representative sequence (or query sequence; in blue) that exhibit partial overlap (in green) (C), and extending the MEMs retained after refinement using the given score matrix (D) to obtain the respective eMEMs. MEM, maximal exact match; eMEM, extended MEM.