Past exam of the mathematical and Computational Biology course of the University of Cambridge / 2024 / Paper 1 / C4 / e / Solution

An affine gap penalty charges a larger opening cost than extension cost, reflecting that a single insertion or deletion event can span several residues. For a gap of length $\ell \ge 1$, explicitly chooseThe supplied sequence alignment has two gap runs, of lengths one and two. Its residue–residue score remains $24$, so this choice givesMore generally, this affine gap penalty convention gives $S=24-2o-e$. There is no unique numerical rescore until opening and extension costs are chosen. A concave length-dependent gap penalty can make very long gaps progressively cheaper per added residue; distinct terminal gap penalties can accommodate incomplete sequence ends. Each choice encodes a different assumption about insertions, deletions or sequence completeness.