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, 17:18, 21 May 2014
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| == Parsimony == | | == Parsimony == |
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− | Parsimony means doing something in the simplest and most economical way. In the context of variant representation, this means representing a variant in as few nucleotides as possible without reducing the length of any allele to 0. It is a property describing the nature of the length of a variant's alleles.
| + | In the context of variant representation, parsimony means representing a variant in as few nucleotides as possible without reducing the length of any allele to 0. It is a property describing the nature of the length of a variant's alleles and is defined as follows: |
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| A variant is parsimonious if it is represented in as few nucleotides as possible | | A variant is parsimonious if it is represented in as few nucleotides as possible |
| without an allele of length 0. | | without an allele of length 0. |
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| + | Also, |
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| + | A variant has superfluous nucleotides on its left side if the leftmost nucleotide of each variant is of the same type |
| + | and the removal of the nucleotide from each allele will not result in an empty allele. |
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| Taking the example below, the Multi Nucleotide Polymorphism (MNP) is represented superfluously for the first 3 representations and parsimoniously for the 4th representation. When a variant has superfluous nucleotides on the left side, it is defined as not being left parsimonious as there is a need to left trim. The concept is symmetric for right parsimony and trimming. Parsimony applies to Indels too which we shall demonstrate in the left alignment section. | | Taking the example below, the Multi Nucleotide Polymorphism (MNP) is represented superfluously for the first 3 representations and parsimoniously for the 4th representation. When a variant has superfluous nucleotides on the left side, it is defined as not being left parsimonious as there is a need to left trim. The concept is symmetric for right parsimony and trimming. Parsimony applies to Indels too which we shall demonstrate in the left alignment section. |