News and Updates
For detailed info click on a branch.
- 4 March - New Transcriptome and Proteome for Stylissa carteri and Xestospongia testudinaria They are available in the DataSets and Blast sections
4th March, 2016 - New Transcriptome and Proteome for Stylissa carteri and Xestospongia testudinaria They are available in the DataSets and Blast sections:
Reference: Hologenome analysis of two marine sponges with different microbiomes. Provided by Taewoo Ryu - APEC Climate Center, Korea.
- 27 January - New Transcriptome and Peptide Predictions for Haliclona amboinensis and Haliclona tubifera
27th January, 2016 - New Transcriptome and Peptide Predictions for Haliclona amboinensis and Haliclona tubifera. They are available in the DataSets and Blast sections:
Authors: Christine Guzman and Cecilia Conaco (cconaco[at]msi.upd.edu.ph). Marine Science Institute, University of the Philippines, College of Science, Diliman, Quezon City, Philippines 1101.
Reference: Guzman, C. and Conaco, C. Comparative transcriptome analysis reveals insights into the streamlined genomes of haplosclerid demosponges. Sci. Rep. 6, 18774; doi: 10.1038/srep18774 (2016).
- 9 April - New DataSets for for Bugula neritina
9th April, 2015 - New DataSets for for Bugula neritina (Transcripts and Protein translations) They are available in the DataSets and Blast sections:
Transcriptome analysis elucidates key developmental components of bryozoan lophophore development (2014) Yue Him Wong; Taewoo Ryu; Loqmane Seridi; [et al.] Nature Publishing Group (NPG). Provided by Taewoo Ryu from the King Abdullah University of Science and Technology (Kingdom of Saudi Arabia).
- 29 October - New DataSets for for Sycon ciliatum and Leucosolenia complicata.
They are available in the DataSets and Blast sections:
Authors: Marcin Adamskifirstname.lastname@example.org, Sven Leininger, Brith Bergum, Jing Liu, Maja Adamska. Sars International Centre for Marine Molecular Biology, Bergen (Norway).
- 22 October - 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
- 18 September - Minor bugs fixed.
Minor bugs fixed in data retrieval.
- 15 January - The Aurelia Project sub-site is open to public access!
The new web site: http://www.compagen.org/aurelia is available.
- 11 September - New Datasets!
New Datasets for Oscarella Carmela and Ephydatia muelleri. (RNA-seq and associated protein models).
Provided by Daniel J. Richter, Jennyfer Mora and Scott A. Nichols (email@example.com - University of Denver).
- 15 November - Links section added.
List of changes:
Links section added. It includes links to external resources.
- 12 October - Compagen 3.0!
List of changes:
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.
- 14 June - Added Oscarella carmela genome and Oscarella sp. transcriptome.
Scott A. Nichols (sa.nichols321[at]gmail.com) from the University of Denver, has provided the following Datasets:
OCAR_WGA_120614: Oscarella carmela whole genome assembly. It was sequenced at ~500x coverage using Illumina paired-end reads from a ~400bp insert library made from DNA that was amplified (whole genome amplification) from a single larva. The assembly was made using SOAP de novo.
OCAR_G-PEP_120614: Oscarella carmela predicted peptides from genome sequencing.
Osp._T-CDS_120614: Oscarella sp. transcriptome. It was sequenced using single-end Illuina reads from mRNA isolated from the somatic tissue of a single adult individual. The assembly was made using Trinity.
Scott A. Nichols (University of Denver) - sa.nichols321[at]gmail.com
Daniel Richter (University of California, Berkeley)
Nicole King (University of California, Berkeley)
- 23 April - Hydra vulgaris AEP transcriptome (454 technology) and new "Tools" section.
HAEP_T-CDS_120217 (Hydra vulgaris AEP transcriptome): Includes assemblies of 454 reads from FACS sorted ectodermal epithelial cells (ECTO), endodermal epithelial cells (ENDO) and i-cells (NANOS). Expression values in these three cell lineages can be viewed and compared using "Atlas Tool".
New "Tools" for working with Hydra vulgaris AEP transcriptome:
Search Tool: Retrieve sequences, expression values and annotations for given contig(s) or keyword(s).
Atlas Tool: Compare gene expression in different cell lineages (ECTO,ENDO,NANOS). In addition contains two reference transcriptomes:
EXT (extended transcriptome): Pooled mRNA from male and female polyps, unfertilized eggs, embryos at various stages, regeneration and budding.
WT (wild type transcriptome): mRNA from polyps without gonads or buds.
SQL Queries Tool: Construct your own queries against AEP transcriptome database. You need to get familiar with SQL syntax, but it will allow any type of customized search. Simple manual about SQL search is included.
NOTE: This is the test release of AEP dataset and "tools" section. Please feel free to report any bugs using the Contact section. We are happy to get feedback and your suggestions.
- 1 December - Compagen 2.0 is here!
We are happy to present a new version of Compagen! Please keep in mind that it is still under development. Please report any bugs here.
List of changes:
- New option to directly View/Download sequences of BLAST hits.
- Raw reads from WGS have been removed (May be added on demand).
- Name convention for the Datasets have been modified. Please check the DataSet section.
- New Datasets added:
BFLO_G-PEP_111130 (Branchiostoma floridae protein models)
HMAG_G-PEP_111130 (Hydra magnapapillata protein models)
NVEC_G-PEP_111130 (Nematostella vectensis protein models)
- Recently published genome data from >Acropora digitifera (Satoh Group OIST Japan) were also added:
ADIG_G-CDS_111201 (transcript models)
ADIG_T-CDS_111201 (transcript models)
ADIG_G-PEP_111201 (protein models)
- Completely new design.
- New version of wwwBlast (2.2.25).
- 4 January - Compagen updated!
After nearly 2 years the basal metazoan datasets have been updated or complemented by newly available data from public resources. Hope everything works ... please report bugs.
New datasets added or updated: (see also Datasets section)
Aiptasia pallida (dbEST_AIPP_100104, dbCAP3_AIPP_100104)
Acropora millepora (dbEST_AMIL_100104, dbCAP3_AMIL_100104)
Acropora palmata (dbEST_APAL_100104, dbCAP3_APAL_100104)
Amphimedon queenslandica (dbEST_AQUE_100104, dbCAP3_AQUE_100104)
Anemonia viridis (dbEST_AVIR_100104, dbCAP3_AVIR_100104)
Clytia hemisphaerica (dbEST_CHEM_100104, dbCAP3_CHEM_100104)
Montastrea faveolata (dbEST_MFAV_100104, dbCAP3_MFAV_100104)
Mnemiopsis leidyi (dbEST_MLEI_100104, dbCAP3_MLEI_100104)
Oscarella carmela (dbEST_OCAR_100104, dbCAP3_OCAR_100104)
Porites astreoides (dbEST_PAST_100104, dbCAP3_PAST_100104)
Pleurobrachia pileus (dbEST_PPIL_100104, dbCAP3_PPIL_100104)
- 8 February - Compagen updated!
www.hydrabase.org is now linked to Compagen!
Monosiga ovata (12.139 CAP3 assembled contigs+singlets)
Metridium senile (29.412 ESTs; 8.284 CAP3 assembled contigs+singlets)
Trichoplax adhaerens (14.571 ESTs; 1.230.612 WGS sequences)
Dugesia japonica (7.362 ESTs)
Dugesia ryukyuensis (8.988 ESTs)
Macrostomum lignano (7.617 ESTs)
Hydra vulgaris (8.993 ESTs; 3.922 CAP3 assembled contigs+singlets)
Strongylocentrotus purpuratus (141.833 ESTs)
Daphnia magna (13.134 ESTs)
Biomphalaria glabrata (52.624 ESTs)
Sponge datasets renamed:
The species of the designated marine sponge Reniera sp. was redetermined as: Amphimedon queenslandica
All corresponding datasets have been renamed to "AQUE".
- 1 September - Compagen starts open access!
Compagen has been moved to a new webserver. Now it can be used without preceding registration procedure.
dbCDS - A new database type has been introduced representing ESTscan based predictions of putative coding regions in CAP3 assembled EST sequence data.
dbCAP3 - New EST assemblies available for Acropora millepora, Acropora palmata, Hydra mag. sf-1, Hydra vulgaris and Hydra vul. AEP.