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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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 Pattern Matching within Intergenic Regions
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The CGD Pattern Match tool now supports queries of the potential regulatory regions located between annotated features, in addition to the other chromosome- and feature-based sequence sets provided. To utilize this new feature, select "Intergenic regions" from the Sequence Database menu on the tool interface. You can search for specific sequence matches or for sequence patterns, using the character codes listed on the PatMatch tool page.
(Posted September 1, 2010)
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CGD Curation News
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New
Candida albicans Strains page at CGD
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We have added a "Candida albicans Strains" page to CGD, with brief descriptions and references for some of the more commonly used laboratory strains, as well as a lineage diagram. If you would like to suggest additions, corrections, or updates to this list, please send a message to CGD curators with details.
(Posted July 21, 2010)
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Highlights in Candida Biology
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A new bibliography resource is now
available at CGD. Curators have
compiled a set of references on a
variety of topics relevant to
Candida biology. The reference
lists are intended to provide a brief
overview of each subject area, including
many key reviews, and to serve as a
resource for those new to research in
Candida biology.
(Posted July 15, 2010)
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Sequences for Additional Candida-related Species and Strains Now Available
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CGD now provides for download sequences from several Candida
and Candida-related species and strains in addition to C.
albicans SC5314. The new additions include:
- Candida albicans WO-1
- Candida dubliniensis CD36
- Candida glabrata CBS138
- Candida guilliermondii ATCC 6260
- Candida lusitaniae ATCC 42720
- Candida parapsilosis CDC 317
- Candida tropicalis MYA-3404
- Debaryomyces hansenii CBS767
- Lodderomyces elongisporus NRLL YB-4239
All sequences are available on the
Sequence Downloads Page. See the
Sequence Help Page for additional information.
We will add additional strains and species as their genomic sequences become available.
(Posted July 8, 2010)
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New search options on Locus Summary pages
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We have added two new search options to the
"Literature" pull-down menu on each Locus Summary page
(located directly below the GBrowse links on the
right-hand sidebar). The "Full-text lit. search, gene
name(s)" and "Full-text lit. search, gene name(s) and aliases" options
link to the Textpresso tool, which supports searches
of the full text of Candida albicans papers in CGD. The
"gene name(s)" search pre-fills the keyword search box
with the standard and systematic name of the gene,
whereas the "gene name(s) and aliases" search also
includes all of the gene synonyms or aliases listed in
CGD. (Posted April 22, 2010)
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Links to Candida Gene Order Browser
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CGD now links to the Candida Gene Order Browser (CGOB), which is an online tool for visualizing the syntenic context of genes from multiple Candida genomes. A link to the synteny view for each C. albicans gene appears in the "External Links" section of the CGD Locus Summary Page. CGOB is developed by David Fitzpatrick and Geraldine Butler at the University College Dublin, Ireland.
(Posted April 13, 2010)
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Updated
comparisons to S. cerevisiae
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Ortholog and Best Hit mappings of
C. albicans genes to S. cerevisiae genes
have been updated
based on the latest Assembly 21 sequence of the
C. albicans genome and the latest annotation at
the Saccharomyces Genome Database (SGD). These appear as hyperlinks between
CGD Locus Pages and the corresponding Locus Pages at
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 homolog directory on
the CGD Downloads site. Gene Ontology (GO) annotations have also been updated at CGD based on the
updated S. cerevisiae ortholog mappings and
the latest GO information at SGD. The procedure used for the transfer of GO annotations is described in further
detail here. Based on orthology, we have inferred 13,424 GO annotations for 3,324 C. albicans genes in CGD.
(Posted March 30, 2009)
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CGD now contains comprehensive Gene Ontology annotations for C. albicans gene products
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CGD curators have reviewed all of the gene-specific literature for C. albicans and are curating the new literature on an ongoing basis. Because all of the available literature has been considered, we have now assigned Gene Ontology (GO) annotations to the root terms "molecular_function unknown", "biological_process unknown", or "cellular_component unknown" to gene products for which there are no experimental or computational data that would allow annotation with a non-unknown GO term. The evidence code for these "unknown" annotations, ND (No biological Data available), indicates that curators have searched for but have not found any relevant information as of the annotation date. CGD is now "GO complete", meaning that each gene product has a GO annotation (including unknowns) in each of the three GO aspects.
(Posted March 11, 2010)
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Expanded phenotype data and new curation system in CGD
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CGD is now releasing our improved and
expanded mutant phenotype pages. We have implemented a
controlled-vocabulary system for phenotype curation that is already in
use by AspGD and SGD. This system greatly
increases the amount of detailed information that can be captured for
each phenotype, and facilitates searching and comparison of mutant
phenotypes. Each phenotype annotation contains a term representing the
entity or process that is observed (e.g., hyphal growth, carbon source
utilization, virulence; view the
complete list) and a qualifier that describes the effect on that
entity or process in the mutant (e.g., decreased, increased,
abnormal). Additional fields display information such as strain
background, allele name, conditions under which the phenotype is
observed, or the identity of relevant chemicals. A brief version of
the phenotype is displayed on the Locus Summary page for each gene,
and the complete information is accessible via the 'Phenotype' tab at
the top of the page. All of the information is searchable via CGD's
Quick Search and Expanded
Phenotype Search, and may also be downloaded in bulk using CGD's
Batch Download tool or Download Data page.
(Posted February 24, 2010)
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February 17 Power Outage
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Access to the Candida, Aspergillus, and Saccharomyces Genome Databases was disrupted on Wednesday, February 17, when a plane crash caused a day-long power outage in the city of Palo Alto, forcing an emergency shutdown of our servers. Power has now been restored, and our web sites are back online.
(Posted February 18, 2010)
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CGD Protein Information Pages now available
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CGD has expanded to include protein information for all verified
and predicted ORFs. Using software and database tools developed at the
Saccharomyces Genome Database (SGD),
the Protein Information Pages display basic property, domain organization,
structural and homology information. To view the page for a given protein,
navigate to the Locus Summary page for the corresponding gene and click on the
"Protein" tab towards the top of the page.
Example Protein Pages:
Act1p;
Cdc28p;
Orf19.4531p.
(Posted February 5, 2010)
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CGD hosts phenotype images and viewer from Homann et al. study
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A collection of 100,000 images representing the mutant phenotypes reported in Homann et al. (2009) A phenotypic profile of the Candida albicans regulatory network. PLoS Genet 5(12):e1000783 is now available at CGD, along with a Java application that allows searching and viewing of the images. In this study, the phenotypes of 143 homozygous null mutant strains, each deleted for a known or putative transcription factor gene, were assayed under multiple conditions. To access these images, download and install the Phenotype Viewer software (available in both PC/Linux and Mac versions). We thank Oliver Homann for providing the data and application and for help in incorporating the data into CGD. (posted January 13, 2010)
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Registration now open for the 10th ASM Conference on Candida and Candidiasis
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The 10th ASM Conference on
Candida and Candidiasis will
take place from March 22-26, 2010, at
the Hyatt Regency in Miami, Florida.
Registration and abstract submissions
are now open, at the meeting
web site. Abstracts are due by
January 15, 2010.
(Posted December 17, 2009)
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Updated
comparisons to S. cerevisiae
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Ortholog and Best Hit mappings of
C. albicans genes to S. cerevisiae genes
have been updated
based on the latest Assembly 21 sequence of the
C. albicans genome and the latest annotation at
the Saccharomyces Genome Database (SGD). These appear as hyperlinks between
CGD Locus Pages and the corresponding Locus Pages at
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 homolog directory on
the CGD Downloads site. Gene Ontology (GO) annotations have also been updated at CGD based on the
updated S. cerevisiae ortholog mappings and
the latest GO information at SGD. The procedure used for the transfer of GO annotations is described in further
detail here. Based on orthology, we have inferred 13202 GO annotations for 3314 C. albicans genes in CGD.
(Posted December 3, 2009)
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CGD paper in Nucleic Acids Research Database Issue
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A paper entitled "New tools at the Candida Genome Database:
biochemical pathways and full-text literature
search" will appear in the 2010 Database Issue
of Nucleic Acids Research. The paper is now
available
online as a Nucleic Acids Research Advance
Access article.
(Posted October 7, 2009)
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Three new resources for the Candida community
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Carol Munro, University of Aberdeen, and Christophe d'Enfert, Institut
Pasteur, have recently received funding from the Wellcome Trust, UK to
create three new resources for the Candida community. The three
main goals of the project will be to create (1) a C. albicans
ORFeome library by cloning every predicted ORF into a Gateway®
vector in E. coli, (2) a library of bar-coded
C. albicans over-expression vectors by placing each ORF under
the control of a reverse Tetracycline promoter in a C. albicans
integrative plasmid based on CIp10 and (3) a library of
C. albicans strains each over-expressing a single gene by
integrating the plasmids generated in (2) into the RPS1 chromosomal
locus. Each ORF will be verified by sequencing both ends. The funding
ends in September 2012 and at this point the 3 collections will be
made available to the community and distributed for a small fee that
will cover maintenance and distribution costs. Contact Carol Munro (c.a.munro@abdn.ac.uk) or
Christophe d'Enfert (christophe.denfert@pasteur.fr) for more information. (Posted September 29, 2009)
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10th ASM Conference on Candida and Candidiasis
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The 10th ASM Conference on Candida and Candidiasis will take place from March 22-26, 2010, at the Hyatt Regency in Miami Florida. Abstract submissions will open in Fall 2009. Please see the meeting web site for details.
(Posted May 10, 2009)
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Search full text of Candida journal articles with Textpresso
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A full-text literature search capability has now been added to CGD. The literature search tool is powered by Textpresso, a text-mining tool developed at Wormbase (Muller H, et al. (2004) PLoS
Biol. 2(11):e309). Currently, the application contains over 16,500 Candida-related full-text journal articles. The full-text literature search can be accessed via the Full-text Search link on the sidebar on the CGD home page, and is also available as a link on the Search Options contents page.
(Posted April 14, 2009)
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CGD
grant renewal
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We are very pleased to announce that the National Institute of Dental & Craniofacial Research at the US National Institutes of Health has renewed the grant that funds CGD. We thank the many members of the scientific community who made this possible by writing letters of support. We look forward to another five years of service to the Candida research community.
(Posted April 2, 2009)
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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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