title: Protein domain recurrence and order can enhance prediction of protein functions.
abstract: BACKGROUND
  Burgeoning sequencing technologies have generated massive amounts of genomic and proteomic data. Annotating the functions of proteins identified in this data has become a big and crucial problem. Various computational methods have been developed to infer the protein functions based on either the sequences or domains of proteins. The existing methods, however, ignore the recurrence and the order of the protein domains in this function inference.
  
  
  RESULTS
  We developed two new methods to infer protein functions based on protein domain recurrence and domain order. Our first method, DRDO, calculates the posterior probability of the Gene Ontology terms based on domain recurrence and domain order information, whereas our second method, DRDO-NB, relies on the naïve Bayes methodology using the same domain architecture information. Our large-scale benchmark comparisons show strong improvements in the accuracy of the protein function inference achieved by our new methods, demonstrating that domain recurrence and order can provide important information for inference of protein functions.
  
  
  BACKGROUND
  The new models are provided as open source programs at http://sfb.kaust.edu.sa/Pages/Software.aspx.
  
  
  BACKGROUND
  dkihara@cs.purdue.edu, xin.gao@kaust.edu.sa
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics Online.
authors.affiliation: Mathematical and Computer Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
authors.forename: Mario Abdel
authors.initials: MA
authors.lastname: Messih
authors.forename: Meghana
authors.initials: M
authors.lastname: Chitale
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kihara
authors.forename: Xin
authors.initials: X
authors.lastname: Gao
mesh_terms: D001499:Bayes Theorem; D015233:Models, Statistical; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000502:physiology*; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins