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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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 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 Curation News
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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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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 12502 GO
annotations for 3282 unique features in CGD.
(Posted March 26, 2009)
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New gene name aliases in CGD
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In order to improve the traceability
of historical names for C. albicans genes, we have incorporated
additional alias names into CGD. Locus tags that were assigned in the
GenBank entries for the original Assembly 19 genomic sequence from the
Stanford Genome Technology Center have been added to CGD Locus Summary
pages for open reading frames. These locus tags are in the format
"CaO19.1234", where the numerals after the period identify the open
reading frame and are the same as those used in the systematic names
such as "orf19.1234". We have also added large sets of identifiers
from CandidaDB and
Entrez
gene. Thanks to Christophe d'Enfert for providing us with the
CandidaDB alias names and their mappings.
(Posted February 20, 2009)
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More convenient sequence download options at CGD
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We have made enhancements to two
tools, Gene/Sequence
Resources and Batch
Download, that increase their
flexibility for downloading the
sequences of multiple genomic
regions. Gene/Sequence Resources now
accepts as input a file containing the
coordinates of multiple chromosomal or
contig regions in order to generate a
file containing those sequences. Batch
Download, which retrieves sequence and
other information for annotated genes
and other features within a specified
region, now allows you to specify a
custom length of upstream and
downstream flanking sequence to be
included with the sequence of each
feature. For more details on these
tools, please click the "Help" button
in the upper right-hand section of
each of the interfaces.
(Posted January 27, 2009)
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New Genome Snapshot resource
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We have created a resource, Genome Snapshot, that provides a
daily count of C. albicans genomic features and a summary of
Gene Ontology (GO) annotations. This page displays a pie chart showing
the number of Verified, Uncharacterized, and Dubious protein coding
genes; an inventory of all the genomic features by chromosome; a
summary of GO annotations; and the distribution of GO annotations for
C. albicans gene products in the Process, Function and
Component Ontologies. There is a link to the Genome Snapshot page on
CGD's Home page under "CGD Curation News", and there are also links in
the "About CGD" section of the left-hand sidebar that appears on CGD's
home page and other index pages, and on the About CGD page. (Posted December 3,
2008)
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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 were updated
based on the latest Assembly 21 sequence 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 homolog directory on the CGD Downloads site.
Gene Ontology (GO) annotations have also been updated at CGD based on the
updated annotations of S. cerevisiae orthologs at
SGD. The procedure used for the transfer of GO annotations is described in further
detail here.
(Posted November 14, 2008)
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CGD usage: Two million hits
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The CGD web site has been accessed
over 2,000,000 times, and as we
celebrate this milestone, CGD would
like to thank the Candida research community for your continued support. (Posted November 11, 2008)
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Multiple updates to Assembly 21 sequence and annotation
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In collaboration with Mike Lin, Christina Cuomo, Manolis Kellis, and their colleagues at the Broad Institute, we have employed 100 Mb of new sequence data for C. albicans strain SC5314 and a comparative genomic analysis of 8 closely related species to make hundreds of updates to the Assembly 21 reference sequence (Butler et al., in preparation; see the CGD Sequence Documentation). New genes have been added to the gene catalog; all artificial "adjustments" to the sequence have been examined and corrected; and the boundaries of coding sequences and introns have been updated. 181 ORFs have been classified as "Dubious" because they are indistinguishable from random sequence; the remaining ORFs have been assigned "Verified" or "Uncharacterized" classifications to indicate whether or not there is experimental evidence for the existence of a gene product.
Updates for each chromosome are enumerated in a Summary Table, which is linked to Chromosome History pages that provide a detailed list of all the updates for each chromosome. The Locus History page for each chromosomal feature that was examined contains a note that describes the changes that were made to that feature. In all, 73 new ORFs and 8 new pseudogenes have been added, the coordinates of 63 ORFs have been updated, and 697 sequence updates have been made. (Posted November 7, 2008)
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Additional formats available for sequence retrieval
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Two additional sequence formats (Decorated FASTA and Numbered
Sequence) are now available via the Gene/Seq Resource tool, and the
sequence retrieval pull-down options from Locus Summary
pages. Decorated FASTA format, provided for genomic DNA sequence of
all CGD features, displays color-coding for different parts of a
selected region, such as coding sequence vs. flanking sequence. The
Numbered sequence format, provided for the Exon(s) only sequence of
coding features, formats the sequence as codons and numbers it
beginning at the start codon. For further details, please refer to the
Gene/Seq Resources help page.
(Posted October 10, 2008)
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CGD Pathways server upgrade
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Candida Biochemical Pathways at CGD have been moved to a new, faster server at http://pathway.candidagenome.org/. Please update any bookmarks or locally stored links to Pathway pages, as the old URL will be discontinued.
(Posted October 7, 2008)
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Assembly 20 moving to
archival storage
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We have removed access to Assembly 20
sequences from the Locus Summary
pages, as well as from GBrowse, and
from most sequence analysis
tools. Assembly 20 datasets will
remain available for BLAST
searches, and the Assembly 20-based
sequence datasets will continue to be
available for download from the CGD web site, but these archival files will not be regularly updated.
(Posted October 7, 2008)
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Links
to RefSeq Nucleotide and Entrez Gene records now available
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Candida albicans genes have been computationally
mapped to RefSeq Nucleotide sequences
and Entrez Gene records based on exact
sequence similarity. Links to the
appropriate RefSeq and Entrez Gene
records are available in the "External
Links" section of CGD Locus Summary
pages (Examples: orf19.6115,
HWP1).
The data are also available for
download from our website.
(Posted October 7, 2008)
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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 multiple
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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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 data are also available for
download from our web site.
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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