Evaluation of annotation strategies using an entire genome sequence.
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.
Iliopoulos
Ioannis
I
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.
Tsoka
Sophia
S
Andrade
Miguel A
MA
Enright
Anton J
AJ
Carroll
Mark
M
Poullet
Patrick
P
Promponas
Vassilis
V
Liakopoulos
Theodore
T
Palaios
Giorgos
G
Pasquier
Claude
C
Hamodrakas
Stavros
S
Tamames
Javier
J
Yagnik
Asutosh T
AT
Tramontano
Anna
A
Devos
Damien
D
Blaschke
Christian
C
Valencia
Alfonso
A
Brett
David
D
Martin
David
D
Leroy
Christophe
C
Rigoutsos
Isidore
I
Sander
Chris
C
Ouzounis
Christos A
CA
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
D001426:Bacterial Proteins