Gap symbol

The gap symbol, represented by '-', is employed in an alignment to encode the insertion or deletion of the symbol to which '-' is aligned.

Whether the gap symbol encodes an insertion or deletion depends on in which direction we are viewing the transformation of one string into the other. Take the very small alignment shown below, in which gap symbols are shown in blue along with their aligned symbols. If we view the alignment as transforming string "AACGTA" into "AGTCT", then the gap symbol in the top augmented string correspond to an insertion of the 'C' into "AGTCT", whereas the two gap symbols in the two bottom strings correspond to deletions of an 'A' and a 'C' from "AACGTA".

Gap Symbol