Compared to Version 2.1, the Version 3.0 has been significantly remodeled, with more species and studies, but with simplified interface:
- Eleven novel species whose interest comes from their evolutionary positions and the fact they do or not possess cilia or centrioles. We included the whole proteomes of Allomyces macrogynus, Apis mellifera, Emiliania huxleyi, Laccaria bicolor, Mortierella verticillata, Ostreococcus tauri (in repalcement of Ostreococcus lucimarinus), Phytophtora infestans, Spizellomyces punctatus and Theileria parva .
- Twenty one new ciliary/centrosomal high throughput studies together with three other non ciliary but related studies.
- Introduction of the encoding compartment of the proteins. Most of them are encoded by the nucleus in eukaryotes, but we attributed the properties of mitochondrion or chloroplast as encoding compartment both in the filters and display.
- Update of the links with OMIM (May 2014)
The interface of Cildb V3.0 has been changed to the version 9 of BioMart, which is much more intuitive than previous ones.
- Due to improvement of the Inparamoid algorithm, we suppressed the in-house homology calculation (filtered best hits) for orthology calculation. There is no orthology choice anymore in the query form.
- Filters have been simplified for easier queries. However, all the properties of each protein can be diplayed as attributes and sorted in a file after export.
Compared to Version 2.0, the new features of Version 2.1 include:
- Four new ciliary/centrosomal high throughput studies.
- Update of the links with OMIM (October 2010)
- Implementation of a Motif search tool
Version 2.0 - July 2010
Compared to Version 1.0, the new features of Version 2.0 include:
- Seven new ciliary/centrosomal high throughput studies.
- Two new studies from acentriolar species, since the relevant organelles are functionally related to higher cell centrosomes: centrosomes of Dictyostelium discoideum and spindle poles of Saccharomyces cerevisiae.
- Eight other non ciliary/centrosomal studies have been incorporated: Microtubule-associated proteomes, spindle proteomes and whole sperm cell proteomes of various species.
- Fifteen novel species whose interest comes from their evolutionary positions and the fact they do or not possess cilia or centrioles. The use of these species will be particularly relevant for comparative genomics. For example, we included the whole proteomes of two diatoms, the acentric Phaeodactylum tricornutum and the centric Thalassiosira pseudonana. This brings up to 33 the number of species in Cildb.
- Suppression of the Filterd Blastp database as a choice of orthology method in BioMart queries, just keeping Inparanoid and Inparanoid and filtered Best Hit. To perform the subtractive genomics queries previously allowed by the Filterd Blastp database, we included Blast e-values as properties that can be filtered and displayed as attibutes. Subtractive genomics can now be performed by filtering according to e-values in a customized way, using e-value cutoff between 0 and 1.
- Update of the links with OMIM (May 2010)
- For users particularly interested in searching candidate genes for partially localized ciliopathies, we added the possibility of filtering the nucleotide positions on Homo Sapiens chromosomes in the BioMart query.
Cildb is a knowledgebase, built by the Paramecium Lab at Gif-sur-Yvette, dedicated to proteins involved in centrioles, centrosomes, basal bodies, cilia and flagella in eukaryotes. Cildb contains the whole proteome of 18 species. Orthology relationships between these proteomes have been calculated using Inparanoid ( O'Brien et al., 2005 ) and each relevant protein has been linked to ciliary studies and to human diseases referenced in the OMIM database.