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This is the home of the Candida Genome Database, a resource for genomic sequence data and gene and protein information for Candida albicans. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health.
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CGD News
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 Batch search
for S. cerevisiae orthologs and best hits now available
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S. cerevisiae orthologs and best hits
can now be searched for mutiple
C. albicans genes using the
Batch
Download Tool. The results of the
batch ortholog and best hit search will be
provided as a tab-delimited file
containing the corresponding S. cerevisiae
gene name and SGDID, along with an
indication of whether the
S. cerevisiae gene is an
ortholog or best hit. Please refer to
the help document here
for further details.
(Posted May 8, 2008)
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CGD User Survey
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In order to better serve the needs of the Candida community, CGD would like to know how you use CGD and to solicit your opinions on future directions. We request that every CGD user fill out a brief survey, which may be taken anonymously, about your use of CGD and the directions in which it should develop. Please click here to take the survey online. CGD staff will also have paper copies of the survey to distribute at the 9th ASM Conference on Candida and Candidiasis, March 24-28. We look forward to meeting you there and to receiving your feedback about CGD.
(Posted March 21, 2008)
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CGD Curation News
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Links to C. dubliniensis orthologs now available
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Orthologs between C. albicans
and C. dubliniensis are now available on the
"Ortholog(s)" section at CGD Locus pages
and hyperlinked to appropriate GeneDB
pages (Examples: ECM331,
MKC1).
The ortholog mappings between
C. albicans and
C. dubliniensis were provided
to CGD by John Gamble and Matthew
Berriman at the Wellcome Trust Sanger
Institute. The C. dubliniensis
orthologs are manually curated
positional orthologs based on synteny.
(Posted May 1, 2008)
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Updated
comparisons to S. cerevisiae
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We have updated CGD's comparisons between C. albicans and
S. cerevisiae protein-coding genes in two different
areas.
Ortholog and Best Hit mappings of
C. albicans genes to S. cerevisiae genes were updated
based on Assembly 21 of the C. albicans genome. These
Orthologs and Best Hits appear as hyperlinks between
CGD Locus Pages and the corresponding Locus Pages at
the Saccharomyces Genome Database (SGD). S. cerevisiae
Best Hits and orthologs are searchable using the Quick
Search or the S. cerevisiae Orthologs and Best Hits
Search tool on the CGD Full Search page, and a file
containing all of the ortholog and Best Hit mappings
may be downloaded from the S. cerevisiae orthologs and
Best Hits directory on the CGD Downloads site.
New Gene Ontology (GO) annotations have been added to CGD based on the
annotations of S. cerevisiae orthologs at
SGD. Annotations in SGD based on direct
experimentation (evidence codes IDA, IPI, IGI, and
IMP) were assigned to the orthologous C. albicans gene
products. The CGD annotations predicted by this
method have the IEA (Inferred from Electronic
Annotation) evidence code and are indicated as
computationally assigned. Annotations that were
redundant with existing CGD manually curated GO terms
or with other newly predicted annotations were removed
from the set. In total, 11191 new annotations were
added to 3113 genes. The procedure used for the
transfer of GO annotations is described in further
detail here.
(Posted April 23, 2008)
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New
Files Available for Download
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CGD metabolic pathway information
is now available in a tab-delimited
file containing pathway names and
lists of the genes that encode enzymes
that participate in each pathway. We
have also posted a file that contains
the entire set of CGD pathway
information in the format that is read
by the Pathway
Tools software from SRI. Both
files are available
for download from our web site.
We have also generated a file of annotations of Candida albicans genes to CGD GO Slim terms. A GO Slim is a small subset of terms from the Gene Ontology that is intended to provide a general
overview without all the fine-grained detail contained in the GO
itself. The CGD Downloads site has a new browsable go/
subdirectory containing files related to the Gene Ontology, including the
GO
annotation (gene_association) file containing the annotation of Candida albicans genes
to terms from the complete Gene Ontology (the most precise and
comprehensive GO annotation file at CGD), the less fine-grained CGD GO Slim
annotations file containing annotation of Candida albicans genes
to GO
Slim terms, and the set of CGD GO Slim
terms themselves.
(Posted April 11, 2008)
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New Links from CGD Locus Pages
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CGD Locus pages are now hyperlinked to additional resources for
Candida gene information. These hyperlinks have been added to
the External Links section, which appears below the sequence
information on each Locus page. The new links entitled "Broad" connect to the Candida
comparative annotation site at the Broad Institute. New
"UniProt/Swiss-Prot" links connect to the corresponding UniProtKB records. In
addition, the "CandidaDB" links in CGD have now been now updated to
connect to the multi-genome version of CandidaDB
at the Institut
Pasteur. CGD thanks Christina Cuomo, Dan Barrell, Kati Laiho,
Christophe d'Enfert, and Tristan Rossignol for their help in establishing these links.
(Posted April 4, 2008)
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Candida Biochemical Pathways are now available at CGD
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Graphical, interactive displays of Candida biochemical pathways are now available at CGD. To access the pathway displays, you may browse from a list
of hyperlinked CGD
pathways, search from the main Pathway
Search page, or click on the links that appear on Locus Summary pages of genes involved in a pathway. The pathways were created using the Pathway Tools
software, which is developed and
maintained by the Bioinformatics Research
Group at SRI International. The pathway predictions are being
manually reviewed and curated at CGD, as described in more detail
on our Pathways Help
page. Pathway curation is an ongoing process, and we
welcome your suggestions for new pathways, or any corrections to metabolic pathway information in CGD.
(Posted March 13, 2008)
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New Features at CGD
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We are very pleased to announce significant enhancements to our web site, which have been implemented in collaboration with the Saccharomyces Genome Database. Some highlights:
We welcome your feedback! (Posted December 4, 2007)
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Previous news items are available from the CGD News Archive
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Note: The Candida Genome Database provides information about the molecular biology of the yeast Candida albicans to researchers. CGD staff are not physicians and cannot give medical advice. Information about pathogenic yeast infections such as candidiasis can be found online in the PubMed database or at the Candidiasis information page at Medline Plus.
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