title: Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure.
abstract: The function annotation process in computational biology has increasingly shifted from the traditional characterization of individual biochemical roles of protein molecules to the system-wide detection of entire metabolic pathways and genomic structures. The so-called genome-aware methods broaden misannotation inconsistencies in genome sequences beyond protein function assignments, encompassing phylogenetic anomalies and artifactual genomic regions. We outline three categories of error propagation in databases by providing striking examples - at various levels of appreciation by the community from traditional to emerging, thus raising awareness for future solutions.
authors.affiliation: Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, PO Box 20537, CY-1678 Nicosia, Cyprus.
authors.forename: Vasilis J
authors.initials: VJ
authors.lastname: Promponas
authors.affiliation: Division of Medical Sciences, University of Crete Medical School, GR-71110 Heraklion, Greece.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Iliopoulos
authors.affiliation: Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece.
authors.forename: Christos A
authors.initials: CA
authors.lastname: Ouzounis
keywords: Error propagation; Genome evolution; Genome structure; Genome-aware methods; Genome-wide annotation; Mis-annotation modeling; Next-generation sequencing; Protein function prediction