The AACompldent tool [37, 45, http://www.expasy.org/tools/aacomp/] compares the experimentally determined amino acid composition (the numbers of each amino acid present in a molecule) of an unknown protein with theoretical compositions of all proteins in SWISS-PROT/TrEMBL. A score quantifying the difference between the compositions of query and database proteins is used to rank the candidate proteins. Estimated pI and Mw, as well as the name of an organism or a taxonomic range, and a keyword which will be matched against the annotation in SWISS-PROT can be used to filter the results. In order to further increase confidence in the identification results, the amino acid composition of a calibration protein analyzed in parallel, and/or a short sequence tag of up to six amino acids known to match the sequence of the unknown protein can be specified if known. Several amino acid constellations are available, accounting for different experimental methods of obtaining amino acid compositions and the sets of amino acids quantified by these methods.
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