Bioinformatics Vol. 19 no. 6 2003
Pages 717-726
© 2003 Oxford University Press
Evaluation of annotation strategies using an entire genome sequence
1 Computational Genomics Group,
The European Bioinformatics Institute, EMBL Cambridge Outstation,
Cambridge CB10 1SD, UK
2 EMBL Heidelberg, D-69012 Heidelberg, Germany
3 Max-Delbrück Centre, D-13122 Berlin, Germany
4 Department of Cell Biology and
Biophysics, University of Athens, GR-15701 Athens, Greece
5 Deparment of Computational Biology, IRBM,
I-00040 Rome, Italy
6 CNB-CSIC, Campus University Autonoma,
E-28049 Madrid, Spain
7 Biotechnology Centre, University of Oslo,
N-0349 Oslo, Norway
8 Whitehead Institute, MIT, Cambridge, MA
02139, USA
9 IBM Research Center, Yorktown Heights, NY
10598, USA
Received on May 22, 2002
; revised on October 29, 2002
; accepted on November 21, 2002
Motivation: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In addition, a performance evaluation of automated systems that attempt to tackle sequence analyses rapidly and reproducibly is generally missing. In order to quantify the accuracy and reproducibility of function assignments on a genome-wide scale, we have re-annotated the entire genome sequence of Chlamydia trachomatis (serovar D), in a collaborative manner.
Results: We have encoded all annotations in a structured format to allow further comparison and data exchange and have used a scale that records the different levels of potential annotation errors according to their propensity to propagate in the database due to transitive function assignments. We conclude that genome annotation may entail a considerable amount of errors, ranging from simple typographical errors to complex sequence analysis problems. The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences.
Availability and supplementary information: http://www.ebi.ac.uk/research/cgg/annotation/cteval/
Contact: ouzounis{at}ebi.ac.uk
* To whom correspondence should be addressed.
INA-EKETA, GR-57001 Thessaloniki, Greece
Computational Biology Center, Memorial Sloan-Kettering Cancer
Center, New York, NY 10021, USA
Aetion Technologies LLC, Worthington, OH 43085, USA
¶ Institut Curie, F-75248 Paris, France
|| CNRS, UMR6543, F-06108 Nice, France
** Alma Bioinformatics, E-28760 Madrid, Spain
Cap Gemini Ernst & Young, London SW1X 7LX,
UK
Univ. of Rome ‘La Sapienza’, I-00185 Rome,
Italy
MWG-Biotech AG, Ebersberg, D-85560 Berlin,
Germany
¶¶ Wellcome Trust Biocentre, Univ. of Dundee, Dundee DD1 5HN, UK
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  G. H. Van Domselaar, P. Stothard, S. Shrivastava, J. A. Cruz, A. Guo, X. Dong, P. Lu, D. Szafron, R. Greiner, and D. S. Wishart BASys: a web server for automated bacterial genome annotation Nucleic Acids Res., July 1, 2005; 33(suppl_2): W455 - W459. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Cruveiller, J. Le Saux, D. Vallenet, A. Lajus, S. Bocs, and C. Medigue MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes Nucleic Acids Res., July 1, 2005; 33(suppl_2): W471 - W479. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. R. Marshall, J. A. Fox, S. L. Butland, B. F. F. Ouellette, F. S. L. Brinkman, and G. F. Tibbits Phylogeny of Na+/Ca2+ exchanger (NCX) genes from genomic data identifies new gene duplications and a new family member in fish species Physiol Genomics, April 14, 2005; 21(2): 161 - 173. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. S. Mikkelsen, J. E. Galagan, and J. P. Mesirov Improving genome annotations using phylogenetic profile anomaly detection Bioinformatics, February 15, 2005; 21(4): 464 - 470. [Abstract] [Full Text] [PDF]
|
|