title: Prediction of protein function and pathways in the genome era.
abstract: The growing number of completely sequenced genomes adds new dimensions to the use of sequence analysis to predict protein function. Compared with the classical knowledge transfer from one protein to a similar sequence (homology-based function prediction), knowledge about the corresponding genes in other genomes (orthology-based function prediction) provides more specific information about the protein's function, while the analysis of the sequence in its genomic context (context-based function prediction) provides information about its functional context. Whereas homology-based methods predict the molecular function of a protein, genomic context methods predict the biological process in which it plays a role. These complementary approaches can be combined to elucidate complete functional networks and biochemical pathways from the genome sequence of an organism. Here we review recent advances in the field of genomic-context based methods of protein function prediction. Techniques are highlighted with examples, including an analysis that combines information from genomic-context with homology to predict a role of the RNase L inhibitor in the maturation of ribosomal RNA.
authors.affiliation: NCMLS, CMBI, Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.
authors.forename: T
authors.initials: T
authors.lastname: Gabaldón
authors.forename: M A
authors.initials: MA
authors.lastname: Huynen
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D019677:Artificial Gene Fusion; D001483:Base Sequence; D018833:Chaperonins / Q000235:genetics / Q000378:metabolism; D002875:Chromosomes / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011506:Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D012335:RNA, Ribosomal / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: C501917:ABCE1 protein, human; D018528:ATP-Binding Cassette Transporters; D011506:Proteins; D012335:RNA, Ribosomal; D018833:Chaperonins