Scoring Matrix Is It Always A Symmetrical One ?
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9.8 years ago
User 5037 ▴ 290

IS scoring matrix always a symmetrical one ? like this ?

   A C G T

A  1 2 0 0

C  2 5 5 2

G  0 5 7 0

T  0 2 0 6

scoring • 3.2k views
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Presumably you mean a scoring matrix in the context of sequence alignment? Please try to improve your questions.

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9.8 years ago

In general there is no reason why a scoring matrix used in dynamic programming has to be symmetric. However, the most commonly used ones are symmetric, for example when making an alignment.

Usually a scoring matrix is chosen because it models a biological situation. If your biological model requires an asymmetric scoring system, then you may use one. The SLIM scoring matrix used to detect homologous transmembrane proteins is asymmetric, for example.

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Entering edit mode
9.8 years ago

Keith is correct that for alignment a symmetric scoring matrix is not necessary, but in general symmetric scoring matrices are used since one does not usually usually have a priori information about the particular pair or sequences/species that would permit use of a asymmetric matrix.

For phylogenetic analysis, asymmetric subsitution matrices are common, especially for time-reversible models when base composition is not uniform.

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I didn't think about phylogenetic cases. Thanks for catching that.