- 1 An improved ParameciumDB interface
- 2 A 75 year old paradox in Paramecium biology resolved
- 3 Other Paramecium species
- 4 Identification of Internal Eliminated Sequences genome-wide
- 5 GBrowse2
- 6 RNAi off-target tool
- 7 Microarray data
- 8 InterPro domains have been updated
- 9 ParameciumDB update and web browser cookies
- 10 A new version of GBrowse
- 11 A Wiki for ParameciumDB
- 12 Orthologs of Paramecium genes were determined for 15 representative eukaryotic genomes, using Inparanoid
- 13 New Tool: BioMart interface for advanced searches
- 14 A new skin for ParameciumDB
- 15 New version of ParameciumDB
- 16 ParameciumDB published in Nucleic Acids Research
- 17 Global trends in whole genome duplications revealed by the ciliate Paramecium tetraurelia
- 18 Symposium in honor of Janine Beisson
- 19 International Paramecium Genomics Meeting
An improved ParameciumDB interface
A 75 year old paradox in Paramecium biology resolved
Deepankar Singh and colleagues (ENS, Paris; Nature, in press) have unraveled the molecular basis of mating type determination and its non-mendelian inheritance in P tetraurelia, P octaurelia and P septaurelia, showing that it involves exaptation of a genome-defence small RNA pathway.
Other Paramecium species
Casey McGrath and colleagues from the Lynch lab (Indiana University) have sequenced and annotated the macronuclear (somatic) genome of several Paramecium species including P biaurelia, P sexaurelia and P caudatum. These and other newly sequenced genomes can be queried using the ParameciumDB Blast Server.
Identification of Internal Eliminated Sequences genome-wide
The genome-wide complement of Paramecium tetraurelia Internal Eliminated Sequences (IES) were identified (Arnaiz et al., PLoS Genetics). These short, unique-copy elements, shown to be remnants of transposons, have been integrated into ParameciumDB.
The latest version of the Generic Genome Browser is now available. This version is faster and it is easy to customize page views without having to reload the page, providing a smoother user experience.
RNAi off-target tool
This tool allows the user to specify a nucleotide sequence and a window size (typically, 23 nt, the size of Paramecium siRNA). The sequence is cut into overlapping windows of the specified size and mapped to the genome, with a choice of 0 to 3 mismatches, using the BWA short read aligner. Useful for designing and interpreting RNAi experiments.
Transcriptome data from genome-wide expression profiling has been added to each gene page and to the Genome Browser. For each experiments, the expression profiles were clustered, and the clusters can be viewed by selecting 'Browse microarray data'.
InterPro domains have been updated
6 February 2009
InterPro domains have been re-calculated using the August 2008 version of the InterPro database. The InterPro domains are attached to the Genoscope gene models (GSPATG...) and are visible in GBrowse.
6 February 2009
ParameciumDB is now using the latest version of the Chado database schema (release 1.0).
If you are experiencing problems with ParameciumDB images, please remove ParameciumDB-related cookies (look for cookies for paramecium.cgm.cnrs-gif.fr).
A new version of GBrowse
10 September 2008
A new, faster version of GBrowse (the Generic Genome Browser) is now available for browsing the scaffolds. Among the new features, draggable tracks, balloon information on mouse-over and click of features, and easier navigation using drag-and-drop.
A Wiki for ParameciumDB
4 September 2008
We have set up a Wiki for Paramecium which is integrated into the ParameciumDB web site. If you are reading this, you are in the Wiki.
We encourage members of the community to:
- go to the Community page and add yourselves to the catalogue of Paramecium labs and researchers.
- add content. The Paramecium Biology section, in particular, needs work.
Orthologs of Paramecium genes were determined for 15 representative eukaryotic genomes, using Inparanoid
27 June 2008
Genoscope gene models were used to calculate orthologs using Inparanoid. The Inparanoid program first determines best reciprocal blast matches between a pair of species, and then creates ortholog groups by adding in-paralogs.
Reference : Remm M, Storm CEV and Sonnhammer ELL (2001). Automatic Clustering of Orthologs and In-paralogs from Pairwise Species Comparisons. JMB, 314:1041-1052.
More information concerning Inparanoid is available here.
Ortholog data is found in ParameciumDB:
- On each gene page.
- Under the Browse menu, "Browse ortholog data".
- As a search filter for BioMart advanced searches.
New Tool: BioMart interface for advanced searches
28 April 2008
- BioMart is a query-oriented data management system with a user-friendly interface, developed at the European Bioinformatics Institute by Arek Kasprzyk and colleagues.
- ParameciumDB has adopted BioMart to enable advanced searches i.e. searches based on multiple criteria.
- ParameciumDB BioMart is available from the Tools menu at the top of every page.
- Use of BioMart is very intuitive. To get started, help is available from ParameciumDB BioMart or from the Using_biomart help page.
A new skin for ParameciumDB
4 July 2007
- The ParameciumDB web site has been re-designed.
- Searching has been simplified, with a search box on every page.
- New information is available.
- The community annotation project has started, and a statistics page provides information about annotation progress.
New version of ParameciumDB
14 December 2006
A faster, more complete version of ParameciumDB incorporates several new features.
- The latestest version of Turnkey/GMODWeb with a new search engine based on clucene.
- A new data model, compatible with Apollo. This is most apparent to the end user in the way in which ohnologs (i.e. paralogs that have arisen through whole genome duplication) are displayed.
- Incorporation of more data, including the EST collection.
- Blast against an expanded choice of databases, including ESTs, raw sequence reads and a set of current peptides that incorporates ongoing human curation of the gene models produced by the Genoscope automated annotation of the Paramecium macronuclear genome.
- Download site for retrieval of sequences, the ParameciumDB chado schema and dumps of the database in SQL or gff3 format.
ParameciumDB published in Nucleic Acids Research
16 November 2006
Arnaiz et al. 2007. ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res 35: Database issue D439-D444. PMID: 17142227
Global trends in whole genome duplications revealed by the ciliate Paramecium tetraurelia
9 November 2006
The Paramecium genome article, published in Nature, describes Whole Genome Shotgun sequencing and assembly of the macronuclear genome and the discovery that the gene repertoire has been shaped by a succession of at least three whole genome duplications in the Paramecium lineage.
Symposium in honor of Janine Beisson
5 May 2006
A one day symposium was held in Gif-sur-Yvette and was attended by many of Janine's friends from France, Poland, England, Switzerland, Germany, Japan and the United States. The scientific program included presentations by Maria Jerka-Dziadosz, Roland Perasso, Eric Myer, Jean-Pierre Mignot, Michel Wright, Piotr Slonimski, Joe Frankel and Keith Gull. Photos of the symposium are available.
International Paramecium Genomics Meeting
3-4 May 2006
The successful completion of the Paramecium genome project was celebrated by extending the European Paramecium Genomics Consortium meeting to an international meeting that was held in Dourdan, France. The meeting was attended by European, Japanese and North American members of the ciliate molecular biology community and many members of the team from the Genoscope - Centre National de Séquençage that carried out the sequencing, annotation and analysis of the genome. Photos of the meeting are available.