Open AccessCandidaDB: a genome database for Candida albicans pathogenomics
Author(s) -
Christophe d’Enfert,
Sophie Goyard,
S. Rodriguez-Arnaveilhe,
Lionel Frangeul,
Louis Jones,
Fredj Tekaia,
Oliver Bader,
A. Albrecht,
Luis Castillo,
Angel Domı́nguez,
Joachim F. Ernst,
Chantal Fradin,
Claude Gaillardin,
Susana García-Sánchez,
Piet W. J. de Groot,
Bernhard Hube,
Frans M. Klis,
Shankarling Krishnamurthy,
Donika Kunze,
M.C. López,
Abigail Mavor,
Nigel Martin,
Ivan Moszer,
Djamila Onésime,
J. Perez-Martin,
Rafael Sentandreu,
Eulogio Valentı́n,
Alistair Brown
Publication year - 2004
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gki124
Subject(s) - genome , biology , candida albicans , genome browser , contig , genetics , genome project , gene , computational biology , sequence assembly , relational database , database , genomics , computer science , transcriptome , gene expression
CandidaDB is a database dedicated to the genome of the most prevalent systemic fungal pathogen of humans, Candida albicans. CandidaDB is based on an annotation of the Stanford Genome Technology Center C.albicans genome sequence data by the European Galar Fungail Consortium. CandidaDB Release 2.0 (June 2004) contains information pertaining to Assembly 19 of the genome of C.albicans strain SC5314. The current release contains 6244 annotated entries corresponding to 130 tRNA genes and 5917 protein-coding genes. For these, it provides tentative functional assignments along with numerous pre-run analyses that can assist the researcher in the evaluation of gene function for the purpose of specific or large-scale analysis. CandidaDB is based on GenoList, a generic relational data schema and a World Wide Web interface that has been adapted to the handling of eukaryotic genomes. The interface allows users to browse easily through genome data and retrieve information. CandidaDB also provides more elaborate tools, such as pattern searching, that are tightly connected to the overall browsing system. As the C.albicans genome is diploid and still incompletely assembled, CandidaDB provides tools to browse the genome by individual supercontigs and to examine information about allelic sequences obtained from complementary contigs. CandidaDB is accessible at http://genolist.pasteur.fr/CandidaDB.