Figure 1

Five representations of a part of an alignment of Pepsin A precursor P00790: (a) probabilistic profile; (b) sequence logo [12]; (c) four textual representations. The IB sequence is more compact than profiles or logos, but retains much of the conservation information lost by other textual formats. In the IB sequence, uppercase letter X represents strong conservation (~80%) of amino acid X, while lowercase x represents low conservation (~50%) of X.