title: Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence.
abstract: BACKGROUND
  Campylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and published in 2000. The original annotation was a milestone in Campylobacter research, but is outdated. We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation.
  
  
  RESULTS
  Re-annotation was carried out using sequence database searches such as FASTA, along with programs such as TMHMM for additional support. The re-annotation also utilises sequence data from additional Campylobacter strains and species not available during the original annotation. Re-annotation was accompanied by a full literature search that was incorporated into the updated EMBL file [EMBL: AL111168]. The C. jejuni NCTC11168 re-annotation reduced the total number of coding sequences from 1654 to 1643, of which 90.0% have additional information regarding the identification of new motifs and/or relevant literature. Re-annotation has led to 18.2% of coding sequence product functions being revised.
  
  
  CONCLUSIONS
  Major updates were made to genes involved in the biosynthesis of important surface structures such as lipooligosaccharide, capsule and both O- and N-linked glycosylation. This re-annotation will be a key resource for Campylobacter research and will also provide a prototype for the re-annotation and re-interpretation of other bacterial genomes.
authors.affiliation: Pathogen Molecular Department, London School of Hygiene & Tropical Medicine, UK. Ozan.gundogdu@lshtm.ac.uk <Ozan.gundogdu@lshtm.ac.uk>
authors.forename: Ozan
authors.initials: O
authors.lastname: Gundogdu
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.forename: Matt T
authors.initials: MT
authors.lastname: Holden
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Nick
authors.initials: N
authors.lastname: Dorrell
authors.forename: Brendan W
authors.initials: BW
authors.lastname: Wren
mesh_terms: D016123:Campylobacter jejuni / Q000235:genetics*; D005798:Genes, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics; D011544:Pseudogenes; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*