page_title: Gap penalty
section_title: Types
hierarchical_section_title: Gap penalty / Types
caption_attribution_description: English: This graph shows the difference between types of gap penalties. The exact numbers will change for different applications but this shows the relative shape of each function.
context_page_description: A Gap penalty is a method of scoring alignments of two or more 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.
caption: This graph shows the difference between types of gap penalties. The exact numbers will change for different applications but this shows the relative shape of each function.
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