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IceLogoIceLogo is a program that generates a sequence logo for aligned peptide sequences. A sequence logo is a histogram-like presentation in which the bars are vertical stacks of symbols. Stack height reflects the level of pattern conservation in aligned peptide sequences, and the height of individual symbols is a measure of their frequency at a given position.Unlike other sequence logo generating programs that rely on Shannon????????s information theory, IceLogo operates based on probability theory. Basically, the algorithm takes the experimental set and compares it with a reference set, which can be configured by the user. These two sets are used in a probability analysis, and the results are shown in the resulting sequence logo.IceLogo's functions are freely available as an API using the SOAP protocol.Science