Editing Sequence motif (section)

====Matrices====
A matrix of numbers containing scores for each residue or nucleotide at each position of a fixed-length motif.  There are two types of weight matrices.
* A position frequency matrix (PFM) records the position-dependent frequency of each residue or nucleotide.  PFMs can be experimentally determined from SELEX experiments or computationally discovered by tools such as MEME using hidden Markov models.
* A [[position weight matrix]] (PWM) contains log odds weights for computing a match score.  A cutoff is needed to specify whether an input sequence matches the motif or not. PWMs are calculated from PFMs. PWMs are also known as PSSMs.

An example of a PFM from the [[TRANSFAC]] database for the transcription factor AP-1:

{| class="wikitable" style="text-align:center; border:5"
! Pos !! A !! C !! G !! T !! IUPAC
|-
| 01 || 6 || 2 || 8 || 1 || R
|-
| 02 || 3 || 5 || 9 || 0 || S
|-
| 03 || 0 || 0 || 0 || 17 || T
|-
| 04 || 0 || 0 || 17 || 0 || G
|-
| 05 || 17 || 0 || 0 || 0 || A
|-
| 06 || 0 || 16 || 0 || 1 || C
|-
| 07 || 3 || 2 || 3 || 9 || T
|-
| 08 || 4 || 7 || 2 || 4 || N
|-
| 09 || 9 || 6 || 1 || 1 || M
|-
| 10 || 4 || 3 || 7 || 3 || N
|-
| 11 || 6 || 3 || 1 || 7 || W
|}

The first column specifies the position, the second column contains the number of occurrences of A at that position, the third column contains the number of occurrences of C at that position, the fourth column contains the number of occurrences of G at that position, the fifth column contains the number of occurrences of T at that position, and the last column contains the IUPAC notation for that position.
Note that the sums of occurrences for A, C, G, and T for each row should be equal because the PFM is derived from aggregating several consensus sequences.