Figure 9

E-strings. (1) The effect of the e-string operator <3,-1,2> on the sequence MQTIF. A positive number n skips n letters, a negative number -n insert n indels. (2) The effect of applying two successive e-strings. In the last line, the result is expressed as a new e-string applied to the original string. (3) We define multiplication on two e-strings as yielding the e-string that is equivalent to applying the two e-strings in order. (4) An alignment path is conventionally represented as a vector of edge types (M, D and I). In this example, MDMIMM, shown above a pairwise alignment, is the path that generates that alignment. The alignment can also be generated by a pair of e-strings (shown to the right). An alignment path is therefore equivalent to a pair of e-strings.