Position-specific scoring matrices PSSMs

Key Words Motif discovery sequence motif sequence pattern protein domain multiple alignment position-specific scoring matrix PSSM position-specific weight matrix PWM transcription factor-binding site transcription factor promoter protein features. 

For the purposes of motif scanning, many motif discovery algorithms also output a position-specific scoring matrix (PSSM), which is often confusingly referred to as a PWM. The entries in a PSSM are usually defined as... 

Fig. 3 Different methods were used to extract features from different regions of the poly(A) signals. NUE near upstream element, CS cleavage site, PSSM position-specific scoring matrix, P/V probability based on first-order inhomogeneous Markov sub-model...

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