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Protocol publication

[…] ating a vast amount of research information performed since the original annotation in 2000 and also integrating data from additional Campylobacter species and strains. Major updates include noteworthy modifications to the 4 main surface structure loci in the genome, 18.2% of genome product functions being updated and 90.0% of all CDSs now having additional information. The inclusion of literature searches and a GO annotation alongside genome wide structural modifications has resulted in C. jejuni NCTC11168 being the most comprehensively annotated Campylobacter genome to date., Manual re-annotation of all previously annotated C. jejuni NCTC11168 CDSs [] was carried out based on results from BLASTP [] and FASTA [] sequence comparisons using non-redundant databases. Re-annotation was based, wherever possible, on characterised proteins or genes []. Additional functional data was provided by using the PFAM [] and PROSITE [] motif databases. New searches carried out in this re-annotation included running RFAM [] database and also the programs TMHMM [] and SIGNALP []., This re-annotation included a complete literature search of all CDS numbers and gene names using PubMed [], HighWire Press [], Scirus [] and Google Scholar []. Artemis software release 8 [] was used during re-annotation. The re-annotated sequence was submitted to the EMBL public database and also to GeneDB [] and CampyDB []. The EMBL file included an 'original' and 'updated' note qualifier, a 'product' qualifier and each CDS represented with a unique 'locus_tag' qualifier. Appropriate 'gene' qualifiers were also present. The GeneDB submission included all the above and extra qualifiers 'colour' and 'literature'. This re-annotation also included for the first time a Gene Ontology […]

Pipeline specifications

Software tools BLASTP, TMHMM, SignalP
Databases campyDB
Organisms Campylobacter jejuni