Question: Scoring Matrix Is It Always A Symmetrical One ?
1
gravatar for User 5037
7.2 years ago by
User 5037290
User 5037290 wrote:

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 • 2.3k views
ADD COMMENTlink modified 7.2 years ago by Casey Bergman17k • written 7.2 years ago by User 5037290

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

ADD REPLYlink written 7.2 years ago by iw9oel_ad6.0k
4
gravatar for iw9oel_ad
7.2 years ago by
iw9oel_ad6.0k
iw9oel_ad6.0k wrote:

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.

ADD COMMENTlink written 7.2 years ago by iw9oel_ad6.0k
3
gravatar for Casey Bergman
7.2 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

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.

ADD COMMENTlink written 7.2 years ago by Casey Bergman17k

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

ADD REPLYlink written 7.2 years ago by iw9oel_ad6.0k
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