title: COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.
abstract: The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼ 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue.
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA 02215, USA.
authors.forename: Yi-Chien
authors.initials: YC
authors.lastname: Chang
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA 02215, USA.
authors.forename: Zhenjun
authors.initials: Z
authors.lastname: Hu
authors.affiliation: Diatom Software LLC, Holliston, MA 01746, USA.
authors.forename: John
authors.initials: J
authors.lastname: Rachlin
authors.affiliation: New England Biolabs, Ipswich, MA 01938-2723, USA.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Anton
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA 02215, USA Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA kasif@bu.edu.
authors.forename: Simon
authors.initials: S
authors.lastname: Kasif
authors.affiliation: New England Biolabs, Ipswich, MA 01938-2723, USA roberts@neb.com.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Roberts
authors.affiliation: Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA steffen@bu.edu.
authors.forename: Martin
authors.initials: M
authors.lastname: Steffen
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology*; D030562:Databases, Protein; D058977:Molecular Sequence Annotation
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins