The higher the column the more useful that position for finding matches in sequences. In each column are shown symbols of the amino acids found at the corresponding position in the motif, with the height of the amino acid proportional to the frequency of that amino acid in the column, and the amino acids shown in decreasing order of abundance from the top of the column. Note that the highest values are for columns with less diversity. The height of each logo position is calculated as the amount by which uncertainly has been decreased by the available data, here the amino acid frequencies in each column of the motif. The relative heights of each amino acid within each column are calculated by determining how much each amino acid has contributed to that decrease.
R c is used as the total height of the logo column.
The above description applies to protein sequences. Sequence logos are also produced for DNA sequences. The methodology is very similar to the above except that there are only 4 possible choices for each logo location. The above method assumes that the sequence pattern is less random than the background or expected sequence variation, and this assumption limits the ability of the method to locate subtle patterns in sequences. When background frequencies are taken into account, and the column frequency is less than the background frequency, it is possible for the information given by a particular residue in a logo column to be negative.