External Resources




circle  Candida Genomes

Candida albicans strain SC5314 genome sequence
Assembly 19: The C. albicans strain SC5314 genome sequence and diploid contig-level assembly by the Stanford Genome Technology Center was published in Jones et al. (2004). View the A19 paper and download the A19 supplementary information and sequence files or the original A19 sequence trace files. (The construction of the sequencing library and sequencing methods are described in Tzung et al. (2001).)
Assembly 21: The haploid chromosomal-level Assembly 21 reference sequence is described in van het Hoog et al. (2007).


Candida albicans strain WO-1 genome project
The genome of C. albicans strain WO-1, sequenced at the Broad Institute as part of the Fungal Genome Initiative (FGI).

Candida albicans strain 1161 genome project
Home page for C. albicans strain 1161 sequencing at the Sanger Institute.

Candida dubliniensis genome project
Home page for C. dubliniensis sequencing at the Sanger Institute.

Candida glabrata genome project
A sequencing project of the Genolevures Consortium.

Candida guilliermondii genome project
The C. guilliermondii genome, sequenced at the Broad Institute as part of the Fungal Genome Initiative (FGI).

Candida lusitaniae genome project
The C. lusitaniae genome, sequenced at the Broad Institute as part of the Fungal Genome Initiative (FGI).

Candida parapsilosis genome project
Home page for C. parapsilosis sequencing at the Sanger Institute.

Candida tropicalis genome project
The C. tropicalis genome, sequenced at the Broad Institute as part of the Fungal Genome Initiative (FGI).

Candida Genome Comparisons
Supplementary data from Butler et al. (2009) for eight Candida genomes. Includes genome characteristics (size, telomeres, centromeres, retrotransposons and repeats, CUG usage, SNPs, etc.), phylogeny, gene families and function (pathogenesis-associated gene families, cell wall, stress response, mating and meiosis, etc.), cross-species comparisons (alignments, synteny). Data are available for download as supplementary material associated with the paper, and from the Broad Institute website.


circle  Candida Resources

Candida albicans pages at the NRC-BRI
Genomic information and tools from the Biotechnology Research Institute (National Research Council, Canada). View Assembly 21 of the C. albicans genome sequence and search the annotation of Assembly 19 generated by the Annotation Working Group, described in the publication by Braun et al., 2005.

CandidaDB
Genomic database for C. albicans and related species, part of the Galar Fungail Consortium project. The previous version of CandidaDB is described in the publication by d'Enfert et al., 2005.

Institute for Candida experimentation at the University of Minnesota
Database containing physical map data and other molecular biology information.


circle  Analysis Tools

PathoYeastract
PathoYeastract (Pathogenic Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of all known regulatory associations between transcription factors (TF) and target genes in pathogenic Candida species, based on hundreds of bibliographic references. Currently, it includes C. albicans and C. glabrata, but addition of six more Candida species is under way. Described in Monteiro et al., 2017.

FungiFun2
Online resource that assigns functional annotations to lists of fungal genes or proteins based on different classification methods (Gene Ontology, Functional Catalog, KEGG) and performs an enrichment analysis to identify significantly enriched pathways or processes, described in Priebe et al., 2015.

Homann et al. Phenotype Viewer
Software and instructions to view phenotype image data reported in Homann et al., 2009.

C. albicans Multilocus Sequence Typing (MLST)
Tools for strain typing and epidemiology, hosted at Imperial College London, and described in M.-E. Bougnoux et al. (2003).

Bioinformatics and Sequence Analysis Tools
Tools on the web site of the Center for Biological Sequence Analysis at the Technical University of Denmark. Gene-finding, RNA splicing, protein modification, protein sorting predictions, and more.

Regulatory Sequence Analysis (RSA) Tools
Tools for analysis of nucleotide sequence patterns in Assembly 19.

Multi-genome Analysis of Positions and Patterns of Elements of Regulation (MAPPER)
Tools for prediction of transcription factor binding sites.

Fungal Genomes BLAST at SGD
BLAST search for sequence similarity within fungal genomes, provided by the Saccharomyces Genome Database.

Microbial Genomes BLAST at NCBI
BLAST search for sequence similarity within microbial genomes.


circle  Research Tools

Candida strains at the Fungal Genetics Stock Center
Request strains from several different mutant collections

Developmental Studies Hybridoma Bank
Collection of hybridomas and their antibodies that in the future will include DSHB-Microbe, a collection of antibodies against C. albicans antigens and those of other microbial pathogens.


circle  Medical Mycology Resources

Candidiasis Information at Medline Plus
Medical information about candidiasis.


circle  Other Fungal Information

Saccharomyces Genome Database
Genome, gene, and protein information for the model yeast Saccharomyces cerevisiae.

Debaryomyces hansenii genome project
A sequencing project of the Genolevures Consortium.

Lodderomyces elongisporus Database
The Lodderomyces elongisporus genome, sequenced at the Broad Institute as part of the Fungal Genome Initiative (FGI).

Cryptococcus neoformans genome project
Home page of the genome sequencing effort for the fungal pathogen C. neoformans at the Stanford Genome Technology Center.

Aspergillus Genome Database
Genome, gene, and protein information for Aspergillus nidulans.

The Aspergillus Website
Database with genomic information on the fungal pathogen Aspergillus fumigatus and clinical information on aspergillosis.

Aspergillus nidulans Database
Home page for the A. nidulans genome project at the Broad Institute, part of the Fungal Genome Initiative (FGI).

Ashbya Genome Database
Genome information for Ashbya gossypii, a hemiascomycete plant pathogen with a small genome that exhibits remarkable synteny with the S. cerevisiae genome.

Magnaporthe grisea Database
Home page for the M. grisea genome project at the Broad Institute, part of the Fungal Genome Initiative (FGI).

Schizosaccharomyces pombe genome project
Complete sequence and annotation of the S. pombe ("fission yeast") genome at the Sanger Institute.

Neurospora crassa Database
Home page for the N. crassa genome project at the Broad Institute, part of the Fungal Genome Initiative (FGI).

Fungal Genetics Stock Center
General fungal information, focusing on filamentous fungi; has links to many fungal genome projects.


circle  Other Resources

GenBank
Sequence repository at the NCBI, Bethesda, Maryland, USA.

EMBL
Sequence repository at the EBI, Hinxton Hall, Cambridge, UK.

DDBJ
Sequence repository at Mishima, Japan.

GenePalette
Software application, freely available to academic users, for visualizing annotated features and other sequence elements in GenBank sequences.

PredictProtein
Program for protein structure prediction, from the Protein Design Group at EMBL.

Gene Ontology
Gene Ontology (GO) Consortium home page.

KEGG
Metabolic reactions and pathways from Kyoto University, Kyoto, Japan.

Nucleic Acids Research Database Issues
Articles about genomic and biological databases.
Papers about CGD were published in the
2010, 2007, and 2005 Database Issues.

Go to NAR Database Issue for:
      2010| 2009| 2008| 2007| 2006| 2005| 2004| 2003| 2002| 2001| 2000| 1999| 1998

circle  CGD Papers

Skrzypek MS, Arnaud MB, Costanzo MC, Inglis DO, Shah P, Binkley G, Miyasato SR, Sherlock G.
New tools at the Candida Genome Database: biochemical pathways and full-text literature search.
Nucleic Acids Res. 2010 Jan;38(Database issue):D428-32.
Available here.


Arnaud MB, Costanzo MC, Shah P, Skrzypek MS, Sherlock G.
Gene Ontology and the annotation of pathogen genomes: the case of Candida albicans.
Trends Microbiol. 2009 Jul 3.
Available here.


Butler G, Rasmussen MD, Lin MF, Santos MA, Sakthikumar S, Munro CA, Rheinbay E, Grabherr M, Forche A, Reedy JL, Agrafioti I, Arnaud MB, Bates S, Brown AJ, Brunke S, Costanzo MC, Fitzpatrick DA, de Groot PW, Harris D, Hoyer LL, Hube B, Klis FM, Kodira C, Lennard N, Logue ME, Martin R, Neiman AM, Nikolaou E, Quail MA, Quinn J, Santos MC, Schmitzberger FF, Sherlock G, Shah P, Silverstein KA, Skrzypek MS, Soll D, Staggs R, Stansfield I, Stumpf MP, Sudbery PE, Srikantha T, Zeng Q, Berman J, Berriman M, Heitman J, Gow NA, Lorenz MC, Birren BW, Kellis M, Cuomo CA.
Evolution of pathogenicity and sexual reproduction in eight Candida genomes.
Nature 459(7247):657-62.
Available here.


Arnaud MB, Costanzo MC, Skrzypek MS, Shah P, Binkley G, Lane C, Miyasato SR, Sherlock G.
Sequence resources at the Candida Genome Database.
Nucleic Acids Res. 2007 Jan; 35(Database issue):D452-6.
Available here.


Costanzo MC, Arnaud MB, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G.
The Candida Genome Database: Facilitating research on Candida albicans molecular biology.
FEMS Yeast Res. 2006 Aug;6(5):671-84.
Available on request.


Arnaud MB, Costanzo MC, Skrzypek MS, Binkley G, Lane C, Miyasato SR, Sherlock G.
The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information.
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D358-63.
Available here.


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