Welcome to Compagen-Japan!
Compagen-Japan is a comparative genomics platform for early branching metazoan animals, maintained in the Marine Genomics Unit in Okinawa Institute of Science and Technology (Japan). It stores various raw and processed sequence datasets along the evolutionary tree from sponges and cnidarians up to the tunicates and lower vertebrates.
The idea is to facilitate access and analysis of genomic and transcriptomic data for workgroups that investigate “non-popular” model organisms without sophisticated online analytical resources. The Databases at CompagenJapan contain selected raw genomic and EST sequence datasets available from public domains (NCBI Trace archive, EST). In addition to the public datasets CompagenJapan also provides already processed data like assembled ESTs and NGS data, Unigene collections or predicted peptides.
Currently this resource functions mainly as a mirror-server to Compagen located in Kiel (Germany).
Latest News
29th October, 2014 - New DataSets for for Sycon ciliatum (Genome, Transcriptome and Protein translations) and Leucosolenia complicata (Transcriptome and Protein translations). They are available in the DataSets and Blast sections:
SCIL_WGA_130802
SCIL_T-CDS_130802
SCIL_T-PEP_130802
LCOM_T-CDS_130802
LCOM_T-PEP_130802
Authors: Marcin Adamski-marcin.r.adamski@gmail.com, Sven Leininger, Brith Bergum, Jing Liu, Maja Adamska. Sars International Centre for Marine Molecular Biology, Bergen (Norway).
22nd October, 2014 - New transcriptome for Clytia hemisphaerica - CHEM_T-CDS_141022. Added to DataSets and Blast sections following publication of the research paper:
Differential Responses to Wnt and PCP Disruption Predict Expression and Developmental Function of Conserved and Novel Genes in a Cnidarian
Lapébie, P., Ruggiero A., Barreau C., Chevalier, S., Chang, P., Dru, P., Houliston E., and Momose T.
PLoS Genetics, 10(9): e1004590. doi:10.1371/journal.pgen.1004590
Latest Updates
18th September, 2014 - Minor bugs fixed in data retrieval.
15th January, 2014 - AURELIA PROJECT, the new sub-site of Compagen, is open to public access following publication of the research paper:
Regulation of Polyp-to-Jellyfish Transition in Aurelia aurita
Björn Fuchs, Wei Wang, Simon Graspeuntner, Yizhu Li, Santiago Insua, Eva-Maria Herbst, Philipp Dirksen, Anna-Marei Böhm, Georg Hemmrich, Felix Sommer, Tomislav Domazet-Lošo, Ulrich C. Klostermeier, Friederike Anton-Erxleben, Philip Rosenstiel, Thomas C.G. Bosch, and Konstantin Khalturin
10.1016/j.cub.2013.12.003
How to use Compagen
DataSets: Sequences in fasta format are available at the DataSets section. The datasets can be viewed or downloaded (.zip compressed) and are classified according to following types:
- EST: Expressed sequence tags (raw reads).
- CAP3: Cap3 assembled sequences.
- T-CDS: Transcript models (contigs) derived from assembled ESTs (Sanger, 454, etc.).
- T-PEP: Predicted peptides from transcriptome assemblies (ESTScan, etc.).
- G-CDS: Transcript models predicted from genome assembly.
- G-PEP: Protein models predicted from genome assembly.
- WGS: Whole genome shotgun (raw reads).
- WGA: Whole genome assembly (contigs / scaffolds).
Blast Server: Perform BLAST search against our DataSets.
Tools: Currently, Search, Expression Atlas and SQL queries tools are available for Hydra vulgaris AEP transcriptome (454 technology).