LogOddsLogo
LogOddsLogo is a web based application designed to make the generation of sequence logos from biological sequence alignments simple. Building upon WebLogo 3 source code, LogOddsLogo uses per-observation multiple-alignment log-odds scores as measures of information content at each logo position. These measures have a proper statistical basis and, particularly for proteins, may outperform earlier measures in recognizing functionally relevant alignment columns.
A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each position within a logo, corresponding to an alignment "column", consist of a stack of letters. The height of the stack indicates the sequence conservation at a position, while the height of each letter within the stack is proportional to the observed frequency of the corresponding amino acid or nucleotide at that position. In general, a sequence logo provides a richer and more precise description of a sequence motif than does a consensus sequence.
Yu YK, Capra JA, Stojmirovic A, Landsman D, Altschul, SF. Log-odds sequence logos. Bioinformatics 31:324-31, (2015).
Altschul SF, Wootton JC, Zaslavsky E, Yu YK. The construction and use of log-odds substitution scores for multiple sequence alignment. PLoS Comput Biol. 6:e1000852, (2010).
Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator. Genome Research 14:1188-1190, (2004).
Schneider TD, Stephens RM. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res. 18:6097-6100, (1990).
We thank Zvezdana Stojmirovic for designing the banner for LogOddsLogo, and Leonardo Marino-RamÃrez, Marc Gwadz, and Narmada Thanki for reviewing the website.
Please direct questions and feedback about LogOddsLogo to Yi-Kuo Yu.