Position-specific Scoring Matrix
A position weight matrix (PWM), also called position-specific weight matrix (PSWM) or position-specific scoring matrix (PSSM), is a commonly used representation of motifs (patterns) in biological sequences.
A PWM is a matrix of score values that gives a weighted match to any given substring of fixed length. It has one row for each symbol of the alphabet, and one column for each position in the pattern. The score assigned by a PWM to a substring is defined as, where represents position in the substring, is the symbol at position in the substring, and is the score in row, column of the matrix. In other words, a PWM score is the sum of position-specific scores for each symbol in the substring.
Read more about Position-specific Scoring Matrix: Basic PWM With Log-likelihoods, Incorporating Background Distribution, Information Content of A PWM, Using PWMs
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“As all historians know, the past is a great darkness, and filled with echoes. Voices may reach us from it; but what they say to us is imbued with the obscurity of the matrix out of which they come; and try as we may, we cannot always decipher them precisely in the clearer light of our day.”
—Margaret Atwood (b. 1939)