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About CGD
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C.
albicans Genome Snapshot,
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glabrata Genome Snapshot,
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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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 Updated tRNA Annotation
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We have updated the annotation of C. albicans and C. glabrata tRNA genes, based on predictions using tRNAscan-SE and comparisons with S. cerevisiae homologs. Changes include modification of intron boundaries for all intron-containing tRNAs of C. glabrata, and annotation strand changes to several C. albicans mitochondrial tRNAs. In addition, tRNA names and aliases have been updated, as outlined in the CGD Nomenclature Guide.
(Posted July 25, 2011)
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11th ASM Conference on Candida and Candidiasis
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The 11th ASM Conference on Candida and Candidiasis will take place from March 29 to April 2, 2012 at the San Francisco Hyatt. Registration and abstract submission will open in Fall 2011. Please see the meeting web site for details.
(Posted July 25, 2011)
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CGD Curation News
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- C.
albicans Genome Snapshot.
- C.
glabrata Genome Snapshot.
- New papers added to CGD this week.
- View Genome-wide Analysis papers in CGD.
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New Additions to Highlights in Candida Biology
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CGD curators have compiled a set of references on a variety of topics relevant to Candida biology. We have recently added new bibliographies and topic areas for C. glabrata. 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 19, 2011)
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Seeking Community Input
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We have completed our curatorial review of the scientific literature about genes from C. albicans and C. glabrata, and would welcome you to review the information posted for the genes with which you are familiar. If there in any information that is inaccurate or incomplete, or if we are missing any references that should be cited, please let us know. We greatly appreciate your help in improving this community resource!
(Posted July 18, 2011)
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CGD is on Facebook
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CGD now has its own page
on Facebook, where we will post
occasional updates and announcements.
To see the CGD posts in your
Facebook news feed, you may "like" the page. (Posted July 8, 2011)
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Introducing Multispecies CGD, with
C. glabrata and C. albicans Curation
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We are pleased to announce that we have now fully integrated
C. glabrata information into CGD. We have curated the
entire published experimental literature that describes
C. glabrata genes, as well as the C. albicans literature, and have made extensive updates to the CGD database and software to store and query information across multiple species simultaneously.
New and updated functionalities include:
- Each C. glabrata CBS138 gene has its own Locus Summary page in CGD; see, for example, the C. glabrata CDR1/CAGL0M01760g Locus Summary page.
- The CGD Locus Summary pages for each gene, in C. glabrata as well as C. albicans, contain a newly expanded section describing orthology within the Candida, as well as orthologs in S. cerevisiae. Hyperlinks connect the CGD Locus Summary pages between orthologous C. albicans and C. glabrata genes.
- We have curated the entire published experimental literature that describes C. glabrata genes, and have written gene descriptions, compiled citation lists, assigned Gene Ontology (GO) terms, and collected mutant phenotypes for every characterized gene. We have also leveraged orthology with C. albicans and S. cerevisiae to make predictions about the function, role, and localization of C. glabrata genes that have characterized orthologs in these other species. All of this information is fully available on the CGD web site and in the CGD downloadable files.
- The sequence of the C. glabrata CBS138 genome is available in the CGD searches.
- We have implemented a multispecies BLAST tool, in which any subset of the multiple Candida genomes can be selected and searched simultaneously.
- The CGD Search tools, including the Quick Search, BLAST, Gene/Sequence search, Ortholog Search, and the Pattern Matching Tool, have all been updated to query multiple species.
- Quick Search results are now displayed in sections organized by species. Results that are not species-specific (e.g., individual GO terms, colleagues, references) are listed in a separate section on the results page.
- The Protein Information page (Protein tab) has been updated and reorganized to consolidate the information and links from the Protein Info, Domains/Motifs and Physiochemical Properties subtabs onto a single, more browseable page.
- Genome Snapshots are provided for both C. albicans and for C. glabrata, summarizing the status of the genome annotation on a daily basis.
We welcome your feedback on how we can improve the CGD site and interface to make it more useful for your research. Please contact us any time.
(Posted June, 2011)
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Protein-domain-based Gene Ontology (GO) term predictions in CGD
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We have now added predictions about
gene product function, role, and
localization based on protein domains and motifs. Protein domains were determined using the InterProScan software from the European Bioinformatics Institute (EBI), and then domain-based Gene Ontology (GO) term assignments are made using the InterPro-to-GO mappings from GO Consortium web site.
(Posted June, 2011)
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Links
to PhylomeDB phylogenetic gene trees
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We have added links from CGD to
phylogenetic gene tree pages in PhylomeDB.
PhylomeDB is a public database of gene
phylogenies (phylomes), for exploration of the
evolutionary history of genes through the
visualization of phylogenetic trees and
multiple sequence alignments. You may access
the phylogenetic tree (for example, this
tree for the gene encoding actin) from the
new "PhylomeDB" link in the External Links
section of each gene's Locus Summary page in CGD,
located below the Sequence Information section
on the page. (Posted April 5, 2011)
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Description lines for uncharacterized gene products, based on S. cerevisiae orthologs and predicted Gene Ontology (GO) annotations
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For genes that lack experimental characterization, but which have characterized orthologs in S. cerevisiae, we have now added Description lines to the CGD Locus Summary pages to note the orthology relationships and, where possible, predictions about gene function or localization. The procedures and criteria used to make these predictions are described in more detail here.
(Posted November 22, 2010)
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Sellam et al. (2010) data added to CGD
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A set of new data from a genome-wide experimental annotation study by Sellam et al. (2010) has been added to CGD. Displayed as a GBrowse track are 2,172 previously unknown transcribed regions (see example), with genome-wide occupancy data for RNA polymerases I, II and III shown in the mouse-over window. Also, 49 predicted snoRNA genes are now included in the database. All datafiles are available at the download directory.
Note: if the new track is not initially visible in your browser, refresh the GBrowse display by pressing Reset, which is the bright pink button located in the grey "Instructions" banner near the top of the page.
(Posted October 12, 2010)
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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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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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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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