title: FunCat functional inference with belief propagation and feature integration.
abstract: Pairwise comparison of sequence data is intensively used for automated functional protein annotation, while graphical models emerge as promising candidates for an integration of various heterogeneous features. We designed a model, termed hRMN that integrates different genomic features and implemented a variant of belief propagation for functional annotation transfer. hRMN allows the assignment of multiple functional categories while avoiding common problems in annotation transfer from heterogeneous datasets, such as an independency of the investigated datasets. We benchmarked this system with large-scale annotation transfer (based on the MIPS FunCat ontology) to proteins of the prokaryotes Bacillus subtilis, Helicobacter pylori, Listeria monocytogenes, and Listeria innocua. hRMN consistently outperformed two competitors in annotation of four bacterial genomes. The developed code is available for download at http://mips.gsf.de/proj/bfab/hRMN.html.
authors.affiliation: Helmholtz Zentrum München-German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstrasse 1, Neuherberg, Germany.
authors.forename: Dimitrij
authors.initials: D
authors.lastname: Surmeli
authors.forename: Oliver
authors.initials: O
authors.lastname: Ratmann
authors.forename: Hans-Werner
authors.initials: HW
authors.lastname: Mewes
authors.forename: Igor V
authors.initials: IV
authors.lastname: Tetko
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001412:Bacillus subtilis / Q000235:genetics; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods*; D016680:Genome, Bacterial / Q000235:genetics; D016480:Helicobacter pylori / Q000235:genetics; D020407:Internet; D008087:Listeria / Q000235:genetics; D008089:Listeria monocytogenes / Q000235:genetics; D008390:Markov Chains; D015233:Models, Statistical; D011506:Proteins / Q000145:classification / Q000235:genetics / Q000502:physiology*; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods; D012984:Software
chemical_list: D011506:Proteins