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.
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
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.