title: Evaluation of annotation strategies using an entire genome sequence.
abstract: BACKGROUND
  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.
authors.affiliation: Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Iliopoulos
authors.forename: Sophia
authors.initials: S
authors.lastname: Tsoka
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade
authors.forename: Anton J
authors.initials: AJ
authors.lastname: Enright
authors.forename: Mark
authors.initials: M
authors.lastname: Carroll
authors.forename: Patrick
authors.initials: P
authors.lastname: Poullet
authors.forename: Vassilis
authors.initials: V
authors.lastname: Promponas
authors.forename: Theodore
authors.initials: T
authors.lastname: Liakopoulos
authors.forename: Giorgos
authors.initials: G
authors.lastname: Palaios
authors.forename: Claude
authors.initials: C
authors.lastname: Pasquier
authors.forename: Stavros
authors.initials: S
authors.lastname: Hamodrakas
authors.forename: Javier
authors.initials: J
authors.lastname: Tamames
authors.forename: Asutosh T
authors.initials: AT
authors.lastname: Yagnik
authors.forename: Anna
authors.initials: A
authors.lastname: Tramontano
authors.forename: Damien
authors.initials: D
authors.lastname: Devos
authors.forename: Christian
authors.initials: C
authors.lastname: Blaschke
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
authors.forename: David
authors.initials: D
authors.lastname: Brett
authors.forename: David
authors.initials: D
authors.lastname: Martin
authors.forename: Christophe
authors.initials: C
authors.lastname: Leroy
authors.forename: Isidore
authors.initials: I
authors.lastname: Rigoutsos
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.forename: Christos A
authors.initials: CA
authors.lastname: Ouzounis
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002692:Chlamydia trachomatis / Q000235:genetics* / Q000378:metabolism; D003628:Database Management Systems; D030541:Databases, Genetic / Q000592:standards; D030562:Databases, Protein / Q000592:standards; D004282:Documentation / Q000379:methods* / Q000592:standards; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D016678:Genome; D016680:Genome, Bacterial; D016247:Information Storage and Retrieval / Q000379:methods* / Q000592:standards; D008969:Molecular Sequence Data; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D001426:Bacterial Proteins