Chlamydiae Genomes Re-Annotation Initiative

Redesign of the initiative in 2015

Few months after the CBRS meeting 2013 and our agreement about a general procedure the situation changed significantly. The NCBI announced their plans to re-annotate all prokaryotic genomes in their RefSeq database. Despite the surprise this was very good news, as we can now join forces with the NCBI, utilize their sophisticated infrastructure and thus reduce the workload on our side.

In 2014 we met several times with the colleagues from NCBI RefSeq, have discussed our aims and their plans. The NCBI is very nterested to collaborate with our initiative, which will also be sort of a pilot project for other organisms. We can now propose an updated procedure for the re-annotation of the chlamydial genomes:

1) Contribution of the NCBI:
- Automatic annotation tools: The RefSeq group provides their automatic NCBI prokaryotic genome annotation pipeline (PGAP), which is an ideal platform facilitating homogeneous and up-to-date structural and functional
genome annotation.
- Annotation transfer from reference to non-reference genomes: The NCBI provides tools for automatic annotation transfer from reference genomes to non-reference genomes.
- Synchronization with protein database: The NCBI synchronizes manual annotations, submitted by scientific communities, automatically with the Uniprot/Swissprot protein database.

(For further information about the current development of submission and re-annotation strategies at the NCBI please check the Material of their latest workshop in Oct 2014:

2) Contributions requested from us:
- Definition of reference genomes: The RefSeq team requests the definition of reference genomes by the community. These should be the genome(s) of a species, for which most literature and functional data exists.
- Manual re-annotation of reference genomes: The RefSeq team requests the improvement of the automatic PGAP-annotations of the reference genomes by the community. Improvements should be based on literature reference and include existence of genes as well as their names and product descriptions.
- Maintenance of re-annotation of reference genomes: To keep high quality of the reference genome annotations, the NCBI requests regular updates (e.g., every year or every 2nd year).

Meeting of the Chlamydiae Genomes Re-Annotation Initiative at the 2015 CBRS meeting in New Orleans


Archive: initial setup of the project in 2013

At the 2013 meeting of the Chlamydia Basic Research Society (CBRS) an initiative for the re-annotation of all chlamydiae genomes has formed. The genomes database, so far residing under this URL, stays online but will permanently become part of this initiative. This site will now host all information and data of the initiative. The genomes database will provide direct access to all re-annotated genomes in any phases of the re-annotation project.

Motivation and concept:

The information about Chlamydiae genomes in the public databases is partially outdated and does not reflect the state of the art in Chlamydiae research. This problem is now really hampering compara­tive analyses, particularly in functional genomics and genetics.

The Chlamydiae Genomes Re-annotation Initiative aims for a community-based re-annotation of all publicly available Chlamydiae genomes. It should be submitted as such to the public databases, re­placing the original annotations. Thereby the whole Chlamydiae research community will bene­fit from up-to-date data e.g. provided by sequence similarity searches and genome data­bases. Furthermore, up-to-date public databases will substantially improve and facilitate future Chlamydiae genome sequencing projects.

Specifically adapted bioinformatic tools will provide a high-quality automatic re-annotation of all publicly available Chlamydiae genomes. This software implements a weighted data integration strategy similar to manual curation. Such re-annotation will not change the numbering (locus tags) of all genes already present in the original annotation (e.g., CT858 will get the gene name CPAF but will keep the locus tag CT858). Manual refinement by the Chlamydiae research community will only need to incorporate specific knowledge from recent literature (and e.g. large-scale omics experiments), and will handle nomenclature issues.

All Chlamydiae researchers are invited to support this initiative and to share their knowledge with the community. Participation will be easy, efficient and adjustable to your availability. All participants will be co-authors on the publication in the end of the project.

In order to sustain database quality, we suggest repeating the re-annotation in regular intervals (e.g. synchronized with the biennial CBRS meetings).


Project schedule



Tasks for coordinating group

Tasks for Chlamydiae research community

Tasks specific for genome record owners



Workshop at CBRS Meeting San Antonio March 19, 2013

Automatic re-annotation


Specify automatic re-annotation procedure

Discuss and decide rules and parameters of automatic re-annotation

Follow (and participate in) the discussion


Perform automatic re-annotation


Check (and correct) putative sequencing errors suggested by annotation software

Manual refinement


Suggest rules for manual refinement

Discuss and decide manual annotation rules

Follow (and participate in) the discussion


Provide re-annotated genomes in easily editable form (Excel, GFF, Genbank)

Manually refine annotations (it has been suggested that M2 should be limited to those who volunteer to annotate whole groups of genes)


Provide refined genomes from M2

Manually refine annotations


Provide refined genomes from M3

Manually refine annotations


Provide refined genomes from M4


Submit re-annotation to public databases (NCBI/EMBL/DDBJ)


Provide pan-genome data and analysis; draft manuscript

Contribute to manuscript

Contribute to manuscript



Submit manuscript



Participate! Join the mailing list:

A mailing list has been created for the Chlamydiae Genomes Re-Annotation Initiative. All relevant information and discussion of the initiative will be communicated via this list. It is technically hosted by the University of Vienna.

Join the online community:

Genome re-annotation session at the 2013 meeting of the Chlamydia Basic Research Society (CBRS) in San Antonio, TX:

Get the material: