Gap penalty
Encyclopedia
Gap penalties are used during sequence alignment
. Gap penalties contribute to the overall score of alignments, and therefore, the size of the gap penalty relative to the entries in the similarity matrix
affects the alignment that is finally selected. Selecting a higher gap penalty will cause less favourable characters to be aligned, to avoid creating as many gaps.
event, than it is to have 10 small gaps of length 1. Affine gap penalties use a gap opening penalty, o, and a gap extension penalty, e. A gap of length l is then given a penalty o + (l-1)e. So that gaps are discouraged, o is almost always negative. Because a few large gaps are better than many small gaps, e, though negative, is almost always less negative than o, so as to encourage gap extension, rather than gap introduction.
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
. Gap penalties contribute to the overall score of alignments, and therefore, the size of the gap penalty relative to the entries in the similarity matrix
Similarity matrix
A similarity matrix is a matrix of scores which express the similarity between two data points. Similarity matrices are strongly related to their counterparts, distance matrices and substitution matrices.-Use in sequence alignment:...
affects the alignment that is finally selected. Selecting a higher gap penalty will cause less favourable characters to be aligned, to avoid creating as many gaps.
Constant gap penalty
Constant gap penalties are the simplest type of gap penalty. The only parameter, d, is added to the alignment score when the gap is first opened. This means that any gap receives the same penalty, regardless of its size.Linear gap penalty
Linear gap penalties have only one parameter, d, which is a penalty per unit length of gap. This is almost always negative, so that the alignment with fewer gaps is favoured over the alignment with more gaps. Under a linear gap penalty, the overall penalty for one large gap is the same as for many small gaps.Affine gap penalty
Some sequences are more likely to have a large gap, rather than many small gaps. For example, a biological sequence is much more likely to have one big gap of length 10, due to a single insertion or deletionGenetic deletion
In genetics, a deletion is a mutation in which a part of a chromosome or a sequence of DNA is missing. Deletion is the loss of genetic material. Any number of nucleotides can be deleted, from a single base to an entire piece of chromosome...
event, than it is to have 10 small gaps of length 1. Affine gap penalties use a gap opening penalty, o, and a gap extension penalty, e. A gap of length l is then given a penalty o + (l-1)e. So that gaps are discouraged, o is almost always negative. Because a few large gaps are better than many small gaps, e, though negative, is almost always less negative than o, so as to encourage gap extension, rather than gap introduction.