Given a scoring scheme, the next problem is how to compare the sequences, decide how similar they are and generate an alignment. This problem may be subdivided into alignment methods for two sequences, multiple alignment methods, and methods that incorporate additional non-sequence information, for example from the tertiary structure of the protein.
The simplest two-sequence comparison methods do not explicitly consider insertions and deletions (gaps). More sophisticated methods make use of dynamic programming to determine the best alignment including gaps (see Section 3.2)