Sequence logos

What is a sequence logo?

A sequence logo is a graphical display of a multiple sequence alignment consisting of colour-coded stacks of letters representing amino acids at successive positions. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment that could otherwise be difficult to perceive.

The total height of a logo position depends on the degree of conservation in the corresponding multiple sequence alignment column. Very conserved alignment columns produce high logo positions.

The height of each letter in a logo position is proportional to the observed frequency of the corresponding amino acid in the alignment column.

The letter of each stack is ordered from most to least frequent, so that it is possible to read the consensus sequence from the top of the stacks.

Schneider T.D., Stephens R.M.
Sequence logos: a new way to display consensus sequences.
Nucleic Acids Res. 1990 Oct 25;18(20):6097-100.
PubMed: 2172928 [Full text] [PDF version]

PROSITE sequence logos

The sequence logos available from the PROSITE WebSite have been build using WebLogo.

'#' in a sequence logo figure means the number of true positive hits detected in UniProtKB/Swiss-Prot used to build the sequence logo. Sequence logos aren't generated if the number of true positive hits in UniProtKB/Swiss-Prot is below five.

For patterns, each position is shown in the logo, whereas for profiles only match positions are considered, i.e. the length of the logo corresponds to the length of the profile.

Crooks G.E., Hon G., Chandonia J.M., Brenner S.E.
WebLogo: a sequence logo generator.
Genome Res. 2004 Jun;14(6):1188-90.
PubMed: 15173120 [Full text] [PDF version]