title: Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release.
abstract: BACKGROUND
  Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications.
  
  
  RESULTS
  Over the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5).
  
  
  CONCLUSIONS
  Over the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms.
authors.affiliation: The Institute for Genomic Research, 9172 Medical Center Drive, Rockville, Maryland 20850, USA. bhaas@tigr.org
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Wortman
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Ronning
authors.forename: Linda I
authors.initials: LI
authors.lastname: Hannick
authors.forename: Roger K
authors.initials: RK
authors.lastname: Smith
authors.forename: Rama
authors.initials: R
authors.lastname: Maiti
authors.forename: Agnes P
authors.initials: AP
authors.lastname: Chan
authors.forename: Chunhui
authors.initials: C
authors.lastname: Yu
authors.forename: Maryam
authors.initials: M
authors.lastname: Farzad
authors.forename: Dongying
authors.initials: D
authors.lastname: Wu
authors.forename: Owen
authors.initials: O
authors.lastname: White
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
mesh_terms: D017398:Alternative Splicing / Q000235:genetics; D017360:Arabidopsis / Q000145:classification* / Q000235:genetics*; D019295:Computational Biology / Q000379:methods* / Q000592:standards; D018745:Genome, Plant / Q000235:genetics*; D008957:Models, Genetic; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D020539:Sequence Analysis, Protein / Q000379:methods*; D014956:Writing
chemical_list: D010940:Plant Proteins