<P> a Gap penalty is a method of scoring alignments of two or more sequences . When aligning sequences, introducing a gaps in the sequences can allow an alignment algorithm to match more terms than a gap-less alignment can . However, minimizing gaps in an alignment is important to create a useful alignment . Too many gaps can cause an alignment to become meaningless . Gap penalties are used to adjust alignment scores based on the number and length of gaps . The five main types of gap penalties are constant, linear, affine, convex, and Profile - based . </P> <Ul> <Li> Genetic sequence alignment - In bioinformatics, gaps are used to account for genetic mutations occurring from insertions or deletions in the sequence, sometimes referred to as indels . Insertions or deletions can occur due to single mutations, unbalanced crossover in meiosis, slipped strand mispairing, and chromosomal translocation . The notion of a gap in an alignment is important in many biological applications, since the insertions or deletions comprise an entire sub-sequence and often occur from a single mutational event . Furthermore, single mutational events can create gaps of different sizes . Therefore, when scoring, the gaps need to be scored as a whole when aligning two sequences of DNA . Considering multiple gaps in a sequence as a larger single gap will reduce the assignment of a high cost to the mutations . For instance, two protein sequences may be relatively similar however, may differ at certain intervals as one protein may have a different subunit compared to the other . Representing these differing sub-sequences as gaps will allow us to treat these cases as "good matches" even though there are long consecutive runs with indel operations in the sequence . Therefore, using a good gap penalty model will avoid low scores in alignments and improve the chances of finding a true alignment . In genetic sequence alignments, gaps are represented as dashes (-) on a protein / DNA sequence alignment . </Li> </Ul>

How many gaps are there in the gap model