Gap penalty
Method of DNA analysis
In DNA analysis, gap penalty is a method of scoring alignments of two or more DNA sequences. When aligning sequences, introducing 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.
Applications
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.
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