Updated (2007) Campylobacter jejuni NCTC11168 genome
The updated annotation file can be saved by using the 'right-click'
mouse button and then saving this file. The default file is called 'Cj_updated.art'
and is ready to use within Artemis
genome analysis software. The updated annotation file has also been submitted
to EBI/EMBL and to GeneDB with the original accession number AL111168.
Manual re-annotation was carried out based on results from BLASTP and
FASTA sequence comparisons using non-redundant databases. Additional functional
data was provided using PFAM, PROSITE and RFAM databases. The programs
TMHMM and SIGNALP were also used for added information. A full literature
search was also carried out on coding sequence (CDS) number and gene name.
The updated annotation file is a 'flat-file' in EMBL (European Molecular
Biology Laboratory) format. This is the European version of representing
sequenced information (as opposed to NCBI/GenBank - U.S.A and DDBJ - Japan).
Each feature (e.g. CDS or misc_feature) has appropriate qualifiers giving
relevant information. The CDS feature has the appropriate base range e.g.
1..1223. File locations are followed by a colour qualifier denoting the
different categories of CDS function. There are now two note qualifiers.
The original note has now been denoted as 'Original (2000) note'. The
updated note has been called 'Updated (2006) note'. This is followed by
a product and gene name where appropriate. The locus_tag qualifier (replacing
the systematic_ID qualifier), denotes the CDS number. A literature qualifier
is also present giving useful papers with a PubMed ID. Each CDS also has
related 'misc_features' denoting motifs present at the time of the re-annotation.
Updated annotation file
This work was carried out in collaboration with the Pathogen Genomics Unit at the Wellcome Trust Sanger Institute.