Welcome to Compagen!
Compagen is a comparative genomics platform for early branching metazoan animals, maintained in the Bosch Laboratory at the University of Kiel. 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 Compagen contain selected raw genomic and EST sequence datasets available from public domains (NCBI Trace archive, EST). In addition to the public datasets Compagen also provides already processed data like CAP3 assembled ESTs, Unigene collections or predicted peptides.
Latest News
23rd April, 2012 - Following publication of the manuscript:
Hemmrich G, K Khalturin, AM Boehm, M Puchert, F Anton-Erxleben, J Wittlieb, UC Klostermeier, P Rosenstiel, HH Oberg, T Domazet-Lošo, T Sugimoto, H Niwa, and TCG Bosch (2012) Molecular signatures of the three stem cell lineages in Hydra and the emergence of stem cell function at the base of multicellularity. Mol. Biol. Evol., doi: 10.1093/molbev/mss134v2
we have updated the DataSets available at Compagen by adding Hydra vulgaris AEP transcriptome (454 technology) sequences. We also have included the "Tools" section. - Check News for details.
Latest Updates
15th November, 2012 - Links section added.
It includes links to external resources.
12th October, 2012 - Compagen 3.0.
Design fixed and improved.
Seq-Retrival section removed.
DataSets section renewed. Selection based on the specie's name.
wwwBlast server updated (v2.2.26).
News section updated with a timeline.
CSV Data retrieval system updated.
14th June, 2012 - Added Oscarella carmela genome and Oscarella sp. transcriptome provided by Scott A. Nichols (University of Denver).
Authors:
Scott A. Nichols (University of Denver). - sa.nichols321[at]gmail.com
Daniel Richter (University of California, Berkeley).
Nicole King (University of California, Berkeley).
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).