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Protocols

ParameciumDB specifications

Information


Unique identifier OMICS_19268
Name ParameciumDB
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ParameciumDB

Maintainer


  • person_outline Linda Sperling

Publications for ParameciumDB

ParameciumDB citations

 (10)
call_split

Sfr1, a Tetrahymena thermophila Sfi1 Repeat Protein, Modulates the Production of Cortical Row Basal Bodies

2016
PMCID: 5112337
PMID: 27904881
DOI: 10.1128/mSphere.00257-16
call_split See protocol

[…] y name (“Sfr1”) in addition to its TTHERM identifier. The Tetrahymena Sfr1 protein sequence was used as the query sequence for a BLAST search of the P. tetraurelia genome (Paramecium Genome Database [ParameciumDB]) to uncover the Paramecium Sfr1 homologue (GSPATP00030126001), which serves as the reciprocal best BLAST hit. Multiple-sequence alignment of the two Sfr1 homologues and box shading of re […]

library_books

TFIIS Dependent Non coding Transcription Regulates Developmental Genome Rearrangements

2015
PLoS Genet
PMCID: 4503560
PMID: 26177014
DOI: 10.1371/journal.pgen.1005383

[…] In order to find putative Paramecium TFIIS homologs, BLASTp and tBLASTn searches were performed against a library of predicted proteins and the P. tetraurelia somatic genome, respectively (ParameciumDB, []), using the sequence of Dst1p, the sole TFIIS present in S. cerevisiae []. We identified six genes encoding TFIIS-like proteins, representing four evolutionarily distant TFIIS familie […]

library_books

Genome Wide Analysis of the Phosphoinositide Kinome from Two Ciliates Reveals Novel Evolutionary Links for Phosphoinositide Kinases in Eukaryotic Cells

2013
PLoS One
PMCID: 3823935
PMID: 24244373
DOI: 10.1371/journal.pone.0078848

[…] ed gene since the PIPKc-like domain is not expressed at all as judged by RNA sequencing . Paramecium PIKs were subsequently identified by BLASTP searches with representative TtPIKs and retrieved from ParameciumDB (http://paramecium.cgm.cnrs-gif.fr/) . Reciprocal BLASTP searches with representative PtPIKs at the non-redundant database of NCBI retrieved all identified ciliate PIKs. Predicted gene pr […]

library_books

Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef Building Corals

2012
PLoS One
PMCID: 3329448
PMID: 22529998
DOI: 10.1371/journal.pone.0035269

[…] number of sequences: 165,532). Finally, all protein sequences from selected outgroup taxa were included in the analysis: Plasmodium falciparum and P. vivax from PlasmoDB , Paramecium tetraurelia from ParameciumDB , and Thalassiosira pseudonana, Arabidopsis thaliana, Drosophila melanogaster and human from BioMart . Outgroup protein sequences were analyzed with HMMER as described above. […]

library_books

Identification of Intracellular and Plasma Membrane Calcium Channel Homologues in Pathogenic Parasites

2011
PLoS One
PMCID: 3194816
PMID: 22022573
DOI: 10.1371/journal.pone.0026218

[…] nd C. intestinalis were carried out against the National Center for Biotechnology (NCBI) genomic protein databases. Searches of the P. tetraurelia genome were carried out using the BLASTP facility of ParameciumDB (v.1.59) (http://paramecium.cgm.cnrs-gif.fr) to search the protein database (version 1, published 2006). The S. mansoni genome was searched using the BLASTP search facility of GeneDB (ht […]

call_split

Highly Precise and Developmentally Programmed Genome Assembly in Paramecium Requires Ligase IV–Dependent End Joining

2011
PLoS Genet
PMCID: 3077386
PMID: 21533177
DOI: 10.1371/journal.pgen.1002049
call_split See protocol

[…] LIG and XRCC4 genes were identified in the macronuclear genome of P. tetraurelia by BLAST searches at ParameciumDB (http://paramecium.cgm.cnrs-gif.fr/) . For DNA ligases, we first selected the genes that blasted against ligase genes from other organisms in the automated annotation of the MAC genome se […]

Citations

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ParameciumDB institution(s)
Centre de Génétique Moléculaire, CNRS FRE3144, Gif-sur-Yvette, France; Université Paris-Sud 11, Orsay, France
ParameciumDB funding source(s)
Supported by the Centre National de la Recherche Scientifique and the Agence National de la Recherche (project ParaDice ANR-08- BLAN-0233).

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