Example of generation of a derived model. The original model on the left (for Smith-Waterman-Gotoh) is used to generate the derived model on the right for joining two adjacent HSPs. Extra transitions are allowed from the START state to the INSERT and DELETE states and onto the END state, as the derived model must allow gaps to open directly from the HSPs (in contrast to Smith-Waterman-Gotoh where an alignment cannot start with a gap). Additionally, the original model is local, but in this case the derived model is global, as it must start and end on the HSP.
Slater and Birney BMC Bioinformatics 2005 6:31 doi:10.1186/1471-2105-6-31