Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release.
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.
Haas
Brian J
BJ
The Institute for Genomic Research, 9172 Medical Center Drive, Rockville, Maryland 20850, USA. bhaas@tigr.org
Wortman
Jennifer R
JR
Ronning
Catherine M
CM
Hannick
Linda I
LI
Smith
Roger K
RK
Maiti
Rama
R
Chan
Agnes P
AP
Yu
Chunhui
C
Farzad
Maryam
M
Wu
Dongying
D
White
Owen
O
Town
Christopher D
CD
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
D010940:Plant Proteins