Gap Penalty

Gap penalty values are designed to reduce the score when an alignment has been disturbed by indels. Typically the central elements used to measure the score of an alignment have been matches, mismatches and spaces. Another important element to measure alignment scores are gaps. A gap is a consecutive run of spaces in an alignment and are used to create alignments that are better conformed to underlying biological models and more closely fit patterns that one expects to find in meaningful alignments. Gaps are represented as dashes on a protein/DNA sequence alignment. The length of a gap is scored by the number of indels (insertions/deletions) in the sequence alignment. In protein and DNA sequence matching, two sequences are aligned to determine if they have a segment each that is significantly similar. A local alignment score is assigned according to the quality of the matches in the alignment subtracted by penalties for gaps present within the alignment. The best gap costs to use with a given substitution matrix are determined empirically. Gap penalties are used with local alignment that match a contiguous sub-sequence of the first sequence with a contiguous sub-sequence of the second sequence. When comparing proteins, one uses a similarity matrix which assigns a score to each possible residue. The score should be positive for similar residues and negative for dissimilar residues pair. Gaps are usually penalized using a linear gap function that assigns an initial penalty for a gap opening, and an additional penalty for gap extensions which increase the gap length.