New and Noteworthy
CGD Service Interuption
Over the 2021 Holiday Break, Stanford blocked CGD's servers from the internet
citing security concerns. We are currently in the process of moving CGD to AWS. In
the mean time, you may notice that some features are missing and some tools are
not fully functional. We are working to restore full functionality as soon as
We apologize for the disruptions this has caused.
(Posted January 3, 2022)
CGD Curation News
2022 FEBS Advanced Lecture Course
2022 FEBS Advanced Lecture Course on Molecular Mechanisms of Host-pathogen Interactions
and Virulence in Human Fungal Pathogens is now scheduled for an in person meeting next May in La Colle sur Loup (France).
Registration is now open at the Meeting website. The registration deadline is February 1st, 2022.
(Posted November 1, 2021)
CANDIDA AND CANDIDIASIS 2021
The Candida and Candidiasis 2021 meeting will take place online on March 21 - 27. Previously accepted presenters have been offered the opportunity to present their work at this meeting. New abstracts can also be submitted at this website. The deadline for new abstract submissions is now extended to Friday, 17 January 2021, 5 pm GMT.
(Posted January 5, 2021)
Frank Odds Obituary
Read Frank Odds obituary written by Neil Gow, available here.
(Posted August 26, 2020)
Candida and Candidiasis 2020 Conference postponed
From the Microbiology Society:
"Due to the continued spread of SARS-CoV-2, the cause of COVID-19, the Council of the Microbiology Society, as Trustees of the Society, have taken the difficult decision to postpone this year’s Candida and Candidiasis Focused Meeting, due to take place from 19–23 April in Montreal, Canada. We are currently unable to say when this event will take place; however, we have spoken this morning to the Chair of the organising committee and will keep you all updated as we know more."
The entire message is available here.
(Posted March 9, 2020)
Candida and Candidiasis 2020 Conference - abstracts due soon
The conference, organized by the Microbiology Society and taking place on April 19-23, 2020, in Montreal, Canada, is a successor to the highly valued ASM conference series that finished in 2018. The abstract submission deadline is on this Thursday, January 9. Visit the conference website to register, submit your abstract and for more information.
(Posted January 6, 2020)
Candida auris Data in CGD
We are pleased to announce the addition of
Candida auris B8441 information into
C. auris B8441 was sequenced by the Centers for Disease Control
and Prevention (Lockhart et al. 2017).
Sequence and annotation were obtained by CGD from
C. auris is the fifth Candida species
for which manually curated data are available in our database, joining
C. albicans, C. glabrata, C. parapsilosis, and
The data loading is complete, and:
We look forward to your feedback on the new C. auris species data in
CGD. (Posted August 27, 2019)
- C. auris B8441 sequence is now available in all
of the CGD tools, including BLAST
- Each C. auris gene now has a Locus Summary page
in the database
- Multiple sequence alignments and phylogenetic trees for
have been updated to include C. auris orthologs
- C. auris genome and annotation is available in the
JBrowse Genome Browsers. In the coming months, we
hope to add large-scale datasets to JBrowse, as they become available
- C. auris genes have been assigned predicted function, process, and localization
annotations (Gene Ontology terms) based on orthology to other Candida species,
and also S. cerevisiae, S. pombe, and A. nidulans
- Protein-coding genes have been assigned predicted annotations based
on protein motifs and domains (InterPro), and solved strutures
of homologous proteins from PDB have been identified
- Manual curation of the published scientific literature about C. auris genes is ongoing,
and experimental data collected from the literature will continue to be added
CGD Grant Renewal - letters of support
As you know, the CGD grant is up for renewal this year and we are going to submit an application to the NIH this summer. We have previously asked members of the community to complete a User Survey to help us formulate future directions for CGD and we greatly appreciate the massive response we have received, with all the invaluable suggestions. We are now asking our users for letters of support to accompany the application. It is very important to demonstrate unequivocally how crucial the continued existence of CGD is to Candida research and to the community. We will greatly appreciate if you can email your letter of support to by June 25 and if you also encourage your colleagues and students to do the same. We are counting on your support.
(Posted May 22, 2019)
Issue with contacting CGD
It was brought to our attention that our CGD Suggestions and Questions form, the one with the reCAPTCHA box, was not working properly. There may have been messages that were inadvertently lost. If you recently tried to contact CGD and never received a response, it is most likely because we have not seen your message. We sincerely apologize for this. The problem is now fixed and we also implemented measures to alert us to this kind of issues in the future.
(Posted February 4, 2019)
Candida glabrata MLST database accepting submissions
Candida glabrata Multi Locus Sequence Typing (MLST) database at PubMLST.org is accepting submissions again.
As of August 2018, the C. glabrata MLST database hosted at pubmlst.org has re-opened its submission pipeline.
They welcome submissions of new alleles and sequence types as well as isolate data from ongoing or published studies.
Also the submission of genome data is possible to place them into the phylogenetic context of the current MLST scheme.
Please visit pubmlst.org/cglabrata for more information.
(Posted August 27, 2018)
C. lusitaniae strain CBS 6936 sequence and BLAST datasets now available at CGD
The sequence and annotation of C. lusitaniae strain CBS 6936, described in
Durrens et al. (2017),
has been made available at CGD.
We provide downloads for
protein domain predictions.
In addition, C. lusitaniae CBS 6936 is included among the datasets searchable
multi-species BLAST tool.
The sequence and annotation were obtained by CGD from
(Posted February 27, 2018)
JBrowse Conservation Tracks
CGD has added tracks in JBrowse showing the evolutionary conservation of genomic features for
C. albicans SC5314,
C. glabrata CBS138,
C. dubliniensis CD36,
C. parapsilosis CDC317.
Conservation is shown in four optional quantitative tracks, representing increasing levels
of evolutionary diversity.
In general, the top level (derived from an alignment of 3 closely related species)
will show the highest levels of conservation, and include intergenic regions, while the lowest level (derived from an
alignment of 12 distantly-related budding yeasts) will show the least conservation, and include only the most
highly-conserved genes and features. Conservation scores were produced with the
(Siepel et al, 2005),
based on whole-genome alignments produced by the program TBA
(Blanchette et al, 2004).
Conservation scores and their underlying alignments and phylogenetic models are available for download
in the CGD downloads directory.
Please see our JBrowse Help Page
for more information about JBrowse at CGD.
(Posted December 20, 2017)
Introducing JBrowse for CGD
CGD has implemented JBrowse, the fast, intuitive, and customizable
genome browser developed by the Generic Model Organism Database project
JBrowse allows users to quickly view large-scale sequence data in a
genomic context, at multiple zoom-levels of resolution, from base pairs
in individual sequence reads to read-density summaries across large
genomic regions. Initially, we have loaded the following datasets:
We will be adding additional high-throughput datasets in the coming months.
- Gene expression in C. albicans in a variety of experimental conditions
from Bruno et al, 2010
- Gene expression in C. glabrata in a variety of experimental conditions
from Linde, Duggan et al, 2015
- High-throughput genomic sequence of C. albicans SC5314
from Muzzey et al, 2013,
that was the basis of Assembly 22
JBrowse can be launched from any CGD feature's Locus Summary Page by clicking on the
JBrowse logo about halfway down the page:
The JBrowse window will be centered upon that feature.
Alternately, mouse-over "JBrowse" on the top menu bar of any CGD page, then select and click your
organism of interest in the drop-down menu. The browser window will be centered on an arbitrary location
of the genome.
Please see our JBrowse Help Page
for more details.
(Posted September 29, 2016)
Correction of chromosome 3 haplotype information for C. albicans SC5314 Assembly 22
We have corrected the haplotype assignments on chromosome 3 of C. albicans SC5314,
based on comparisons of haplotype data
(Legrand et al, 2008;
Berman and Forche, 2016)
with sequence data
(Muzzey et al, 2013)
for both the wild-type diploid strain and the strain RBY10-10, which is homozygous for chromosome 3A. This
analysis supported the exchange of approximately 845 kbp between chromosome 3A and chromosome 3B of Assembly 22
at CGD, including the entire left arm of the chromosome, and a portion of the right arm extending from
to within the coding sequence of the gene
This results in sequence and gene model boundary changes for most chromosome 3 features.
(Posted June 22, 2016)
EnsemblFungi gene annotations for Candida strains not curated by CGD
We now provide links on
CGD Homology Pages
and CGD Multi-Genome BLAST results pages
to gene annotations from EnsemblFungi
for the seven Candida-related strains for which we provide sequence
and gene model downloads,
but do not actively curate: C. albicans WO-1, C. guilliermondii ATCC 6260, C. lusitaniae ATCC 42720,
C. orthopsilosis Co 90-125, C. tropicalis MYA-3404, D. hansenii CBS767 and L. elongisporus NRLL YB-4239.
These replace the links to annotations formerly provided by the
Broad Institute Fungal Genome Initiative, which are no longer supported.
(Posted June 6, 2016)
Major update of the C. albicans genome sequence at CGD
We have released a major sequence update for C. albicans SC5314 (Assembly 22, version s06-m01-r01).
Based on reanalysis by CGD of all available sequence data, the update affects more than 300 features,
correcting many ORF translation errors and resolving many sequence ambiguities.
The specific sequence changes can be viewed on our
Chromosome History pages.
(Posted February 2, 2016)
Click here to view archived news items.
CGD Copyright © 2004-2022 The Board of Trustees, Leland Stanford Junior University.
Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. To cite CGD
, please use the following reference
: Skrzypek MS, Binkley J, Binkley G, Miyasato SR, Simison M, Sherlock G (2017). The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data. Nucleic Acids Res 45
(D1); D592-D596; see How to cite CGD.