Dynamic programming recursions for three-profile alignment with affine gap costs Scores for the alignment of two residue positions are denoted by Sp(α, β). The GOP and GEP are gap opening and gap extension penalties, respectively. In affine gap costs, GOP and GEP are fixed values at any residue position.
Hung et al. BMC Genomics 2010 11(Suppl 3):S14 doi:10.1186/1471-2164-11-S3-S14