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| GO Annotations File | ||
| The gene_association.cgd file contains the Gene Ontology (GO) curation from CGD. Please note that this file contains ALL of the CGD GO curation, whereas the gene_association file that is available on the GO consortium (GOC) web site, http://www.geneontology.org/, has been filtered according to GOC guidelines. The file contains curation for current ORFs only (i.e., ORFs that have been deleted from C. albicans Assembly 21 have been omitted from this file). Download the File|View the README | Chromosomal Feature File | |
| The chromosomal_feature file contains information such as names and aliases (synonyms), descriptions, and any S. cerevisiae orthologs for the chromosomal features (including protein-encoding and non-coding genes) in CGD. The information for each curated species in CGD is contained in a separate chromosomal_feature file. Go to the Chromosomal Feature File Directory|View the README | Sequence Files | |
| Files containing
chromosome, contig, ORF, protein, and intergenic sequences
from Candida and Candida-related strains and
species are available for download from this directory. For
species for which older versions of the sequence and
annotation are available (including C. albicans
SC5314), both current sequence data and archived sequence data
may be downloaded. Go to the Sequence Download Directory|View the README | Phenotype data | |
| The
phenotype_data.tab file contains the CGD
phenotype curation, in a tab-delimited table format. The phenotype information for each curated species in CGD is contained in a separate file. Go to the Directory |View the README | Datasets archived at CGD | |
| Access the large-scale datasets from the CGD web site. View the index|Browse the Download Directory | Analyses of C. albicans Assembly 21 | |
| ORFs were mapped from Assemblies 20 and 19 to Assembly 21, and the Assembly 21 files were processed at CGD to identify and classify changes that occurred between assemblies, and to identify other issues, as described in detail on the Sequence documentation page. Files containing all of these analyses (ORF lists, sequences, and/or alignments) are available. Go to the Directory|View the README | Analyses of C. albicans Assembly 20 | |
| Assembly 20 files were processed at CGD to identify and classify changes that occurred between Assembly 19 and Assembly 20, and to identify other features in which users may be interested (e.g., introns/gaps/reading-frame adjustments), as described in detail on the Sequence documentation page. Files containing all of these analyses (ORF lists, sequences, and/or alignments) are available. Go to the Directory|View the README | Supplementary Data for C. albicans Assembly 19 | |
| The supplement to the C. albicans genomic sequencing paper, Jones et al., 2004. Access information about heterozygous polymorphism, raw contigs from the Phrap assembly, sequence omitted from diploid Assembly 19 (rDNA, mtDNA, etc.), and more.
Go to the Index Page | C. albicans Assembly 19 Contig Diagrams | |
| These PDF files depict the the assembly of Contig19's from Contig6's by the Stanford Genome Technology Center (SGTC). These files were originally made available from the Candida web server at the SGTC, and copies are archived here at CGD. Download the Files|View the README | Mappings to external resources | |
| These files contain mappings between CGD features and sequences from external resources, such as Uniprot/Swissprot,
RefSeq and Entrez Gene databases. Download the Files|View the README | Mappings of Historic C. albicans Contigs and ORFs | |
| These files summarize the BLAST-based mapping of ORFs and contigs from older assemblies onto the Assembly 19 contigs and the Assembly 21 and Assembly 20 chromosomes. Go to the Directory|View the README | C. albicans Assembly 6 Aliases | |
| The orf19_orf6_mapping file provides a mapping between the orf6 names assigned during Assembly 6 of the genome sequence and the orf19 names assigned during Assembly 19. Download the File|View the README | C. albicans Assembly 4 Aliases | |
| The orf4_orf19_mapping file provides a mapping between the identifiers from Assembly 4 of the genome sequence and the orf19 names assigned during Assembly 19. Download the File|View the README | GFF files | |
| This directory contains files with information about the features in CGD and features in historic versions of the genome assembly in Generic Feature Format (GFF), as displayed in the GBrowse Genome Browser in CGD. Go to the Directory|View the README | Orthologs and Best Hits | |
| The Orthologs directory contains
the mappings between CGD genes and predicted
orthologs among Candida-related species and in S. cerevisiae and S. pombe. The Orthologs directory also
contains positional orthology mappings between C. albicans and
C. dubliniensis, provided by John Gamble and Matthew Berriman
at the Wellcome Trust Sanger Institute. The Best Hits
directory contains mappings between C. albicans and
S. cerevisiae at a level of similarity below
that required by the strict criteria used to determine orthology. Go to the Orthologs Directory|Go to the Best Hits Directory | Pathway Files | |
| Download files with
information about metabolic pathways from CGD. Go to the Pathways Directory|View the README | Protein Domain Predictions | |
| Output of
IprScan domain predictions for all CGD proteins. Go to the Domains Directory| View the README | Codon Usage Table | |
| The C_albicans_codon_usage file contains a table of calculated codon usage frequencies. View the File and README | Miscellaneous Annotation Files | |
| This directory contains
files that were constructed by CGD in response to a specific
request, but which may be useful to other members of the
research community. The C_albicans_codon_usage.tab file
contains a codon usage table (for Assembly 21). The CGD_GO_genespring_format.tab file
contains Gene Ontology curation in a format for use with GeneSpring software. The orf6_short_desc.txt and orf6_long_desc_plus_GO.txt files contain basic information about genes in CGD from Assemblies 6 and 19 (e.g., orf6 and orf19 names, description information, and GO terms). Go to the Directory|View the README | Community-contributed Data Files | |
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Files contributed by
members of the
community. UAU1_nondisruptable.txt
(from Aaron Mitchell) is a list of C. albicans genes in which
no UAU1 insertions were obtained among at least 12 independent
transformants, suggesting that these genes may be essential (but
conclusive demonstration of essentiality requires additional
experimentation). The GSEA_Nantel_2012 directory contains files for
running Gene Set
Enrichment Analysis (GSEA) on Candida albicans data, provided
to CGD by Andre Nantel. Go to the Directory|View the README | GO Slim file | |
| The goslim_candida.obo file contains the subset of GO
that is used with the GO
Slim Term Mapper tool. The file is best viewed with OBO_Edit, a tool available at the Gene Ontology Consortium website. View the obo file | Candida GO Slim Annotations File | |
| The GOslim_gene_association.cgd file contains GO Slim annotations for CGD genes, using the CGD GO Slim instead of the entire Gene Ontology. A GO Slim is a small subset of terms from the Gene Ontology, which is intended to provide a general overview without all the fine-grained detail contained in the GO itself. For the actual CGD GO curation, please use the gene_association.cgd file. Download the File|View the README | Batch Download Tool | |
| Simultaneously retrieve
multiple types of data for a list of gene or feature names.
Go to the Batch Download Tool page | Browse Downloads | |
| Browse the Download directories on the CGD web site. Go to the top-level directory | ||
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