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 Motif Display Help Page
  A motif is a predominant regulatory sequence theme associated with a specific transcription factor. This collection of common sites can be represented by a consensus sequence, where a lower-case base, for example, signifies a lower degree of frequency compared to an upper-case base. A more accurate display is a position weight matrix (PWM), which gives the probability of each base numerically. A motif can also be displayed graphically as a sequence logo, where the height of each letter is proportional to its frequency at that particular position, but the total height represents the mutual information content. All three methods convey the same underlying information, numerically displayed in the PWM.

Resources and References:

Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990 Oct 25;18(20):6097-100. PMID: 2172928; PMC: PMC332411

Stormo GD. DNA binding sites: representation and discovery. Bioinformatics. 2000 Jan;16(1):16-23. PMID: 10812473