#DOTD: Position-Specific Scoring Matrix

13 Jun 2017

A Position-Specific Scoring Matrix (PSSM) or Position Weight Matrix (PWM) is a matrix which has a width and height corresponding to scores for each letter of the alphabet at each position of the sequence. The score is based on the frequency of that letter in the multiple sequence alignment used to build the matrix, in addition to a model which defines the overall nucleotide composition of the sequence. The score, therefore, represents the probability of each base occurring at each position, not by chance.

 

See these slides for an example.

 

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PhDomics by Fatima