The Unipept web application supports biodiversity analysis of large and complex metaproteome samples. Its underlying index structure is designed to quickly retrieve all occurrences of a tryptic peptide in UniProtKB records. Taxon-specificity of the tryptic peptide is successively derived from these occurrences using a novel lowest common ancestor approach that is robust against taxonomic misarrangements, misidentifications and inaccuracies. Not taking into account this identification noise would otherwise result in drastic loss of information.


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