the relative frequency of each character, the consensus logo depicts the degree of conservation of each position using the height of the consensus character at that position. Advantages and drawbacks The main, and obvious, advantage of consensus logos over sequence logos is their ability to be embedded as text in any Rich Text Format supporting editor/viewer and, therefore, in scientific manuscripts. As described above, the consensus logo is a cross between sequence logos and consensus sequences. As a result, compared to a sequence logo, the consensus logo omits information (the relative contribution of each character to the conservation of that position in the motif/alignment). Hence, a sequence logo should be used preferentially whenever possible. That being said, the need to include graphic figures in order to display sequence logos has perpetuated the use of consensus sequences in scientific manuscripts, even though they fail to convey information on both conservation and frequency. Consensus logos represent therefore an improvement over consensus sequences whenever motif/alignment information has to be constrained to text. Extensions Hidden Markov models (HMMs) not only consider the information content of aligned positions in an alignment, but also of insertions and deletions. In an HMM sequence logo used by Pfam, three rows are added to indicate the frequencies of occupancy (presence) and insertion, as well as the expected insertion length. See also Sequence motif Position-specific scoring matrix DNA binding site References External links Make a Sequence Logo in your browser, offline GitHub Sequence Logo in native Javascript How to read sequence logos. Recommendations for Making Sequence Logos. Erill, I., "A gentle introduction to information content in transcription factor binding sites", Eprint What is (in) a sequence logo? Bioinformatics Statistical charts and diagrams