title: Computational analysis and experimental validation of gene predictions in Toxoplasma gondii.
abstract: BACKGROUND
  Toxoplasma gondii is an obligate intracellular protozoan that infects 20 to 90% of the population. It can cause both acute and chronic infections, many of which are asymptomatic, and, in immunocompromised hosts, can cause fatal infection due to reactivation from an asymptomatic chronic infection. An essential step towards understanding molecular mechanisms controlling transitions between the various life stages and identifying candidate drug targets is to accurately characterize the T. gondii proteome.
  
  
  RESULTS
  We have explored the proteome of T. gondii tachyzoites with high throughput proteomics experiments and by comparison to publicly available cDNA sequence data. Mass spectrometry analysis validated 2,477 gene coding regions with 6,438 possible alternative gene predictions; approximately one third of the T. gondii proteome. The proteomics survey identified 609 proteins that are unique to Toxoplasma as compared to any known species including other Apicomplexan. Computational analysis identified 787 cases of possible gene duplication events and located at least 6,089 gene coding regions. Commonly used gene prediction algorithms produce very disparate sets of protein sequences, with pairwise overlaps ranging from 1.4% to 12%. Through this experimental and computational exercise we benchmarked gene prediction methods and observed false negative rates of 31 to 43%.
  
  
  CONCLUSIONS
  This study not only provides the largest proteomics exploration of the T. gondii proteome, but illustrates how high throughput proteomics experiments can elucidate correct gene structures in genomes.
authors.affiliation: Biodefense Proteomics Research Center, Albert Einstein College of Medicine, Bronx, New York, United States of America.
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Dybas
authors.forename: Carlos J
authors.initials: CJ
authors.lastname: Madrid-Aliste
authors.forename: Fa-Yun
authors.initials: FY
authors.lastname: Che
authors.forename: Edward
authors.initials: E
authors.lastname: Nieves
authors.forename: Dmitry
authors.initials: D
authors.lastname: Rykunov
authors.forename: Ruth Hogue
authors.initials: RH
authors.lastname: Angeletti
authors.forename: Louis M
authors.initials: LM
authors.lastname: Weiss
authors.forename: Kami
authors.initials: K
authors.lastname: Kim
authors.forename: Andras
authors.initials: A
authors.lastname: Fiser
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D017125:Genes, Protozoan / Q000235:genetics*; D016678:Genome / Q000235:genetics; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D020543:Proteome; D040901:Proteomics; D015800:Protozoan Proteins / Q000032:analysis / Q000737:chemistry / Q000235:genetics; D015203:Reproducibility of Results; D017386:Sequence Homology, Amino Acid; D014122:Toxoplasma / Q000235:genetics*
chemical_list: D010455:Peptides; D020543:Proteome; D015800:Protozoan Proteins