CGD Site Map


Contents:



Overview

The CGD site map provides a comprehensive listing of major CGD resources and tools. It is organized by the major categories available at CGD, which correspond to the links located on the left side of the home page. The resources and tools available in that category are listed, followed by a description of the resource and its primary use. A link to the help documentation is also provided, if it is available for that resource.

For more information on how to navigate around CGD, please read the Getting Started page.

Site map

Category Resource Description Primary Use Help Page
Search Options Quick Search and Text Search Search the CGD relational database, including literature guide, colleague information, protein information, and text. Search CGD database using keywords.
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Advanced Search Find a chromosomal feature (e.g., gene, ORF, centromere) based on selected criteria (e.g., chromosome number, GO-Slim terms, etc.) Find chromosomal features that match specific properties or annotations.
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Full-text Literature Search Customizable keyword searching of the full-text of over 16,500 Candida journal articles with Textpresso, a tool developed at Wormbase Search full-text of published papers about Candida.
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Biochemical Pathway Search Search or browse pathway information in CGD, including pathways, reactions, enzymes, and chemical compounds. Find metabolic pathways and related information.
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Expanded Phenotype Search Search the text of all phenotype information to find phenotypes of interest and view the genes associated with them. Enter keywords associated with a phenotype (e.g., 'hyphal', 'virulence') or experimental condition (e.g., 'Spider', 'mouse') to search for features with a specific phenotype.
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Search CGD Web Pages Search CGD HTML pages, excludes the relational database. Find CGD web pages using keywords located on the page.
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List of genome-wide analysis papers Link to a list of genome-wide analysis papers (e.g., microarray analysis publications) curated at CGD. Find CGD curated papers that analyze the entire genome.
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Category Resource Description Primary Use Help Page
Help Resources Getting Started Common uses of CGD for the first time user. Get a brief overview of navigating around CGD.  
FAQ Answers to some of the most frequently asked questions about CGD. Get an answer to a commonly asked question.  
What's New in CGD Changes and additions to CGD resources. Find new resources at CGD and when they were added.  
SGD's Glossary List of terms and definitions at SGD. Find the definition of a new term.  
Category Resource Description Primary Use Help Page
Analysis & Tools BLAST Search Candida DNA and protein sequence datasets for similarities to a particular sequence. Find similarities between a sequence of interest and Candida DNA or protein sequences.
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Gene/Sequence Resources Retrieve Candida genomic sequence from CGD or paste in a DNA or protein sequence to analyze it using numerous CGD resources. Display and analyze a Candida sequence (or other sequence) in many ways.
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GBrowse Genome Browser
C. albicans A22 GBrowse
C. albicans A21 GBrowse
C. albicans A19 GBrowse
C. dubliniensis GBrowse
C. glabrata GBrowse
C. parapsilosis GBrowse
GBrowse allows viewing and navigation of genomic sequence. The GBrowse tool is part of the Generic Model Organism Database Project. Navigate the Assembly 21 and 22 chromosomes, and Assembly 19 contig set. View nucleotide and protein sequence.
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Pattern Matching A pattern matching program that allows ambiguous matches but not gaps. Find short DNA/protein sequence matches in Candida sequences.
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Design Primers Recommends primers appropriate for either PCR or sequencing of a given gene or DNA sequence, within parameters set by the user (end points, Tm, GC/AT ratios, etc.). Design sequencing and PCR primers for Candida or other input sequences.
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Genome Restriction Analysis Generates a restriction map of a specified DNA sequence. The restriction map may include all enzymes, or a subset of enzyme types (3' overhangs, 5' overhangs, blunt ends, or enzymes that cut once or twice). Display restriction maps for Candida or other input sequences.
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SGD's Fungal BLAST Search multiple fungal genomes, including Candida genomes, for similarity to a particular sequence. Find similarities between a sequence of interest and fungal nucleotide or protein sequences.
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Category Resource Description Primary Use Help Page
GO Resources What is GO? SGD help page that explains the philosophy of GO. Get an overview of Gene Ontology (GO).  
SGD's GO Tutorial Tutorial that highlights pages and tools that use GO annotations to familiarize users with the Gene Ontology (GO). Learn where GO annotations are located on CGD pages and how to use them.  
GO Slim Mapper GO Slim is a set of GO terms that represent major sections of the ontology. Gene products are annotated to the most specific GO term possible. This tool traces the specific annotations to their broader GO Slim terms for a given set of CGD genes. Map a set of CGD genes to broad GO Slim categories.
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GO Term Finder Gene products are annotated to the most specific GO terms possible. Common parent terms may not be obvious. This tool determines the GO terms that a set of CGD genes shares in common and graphically displays the significant lineage. Find GO terms that are shared by a group of CGD genes.
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Category Resource Description Primary Use Help Page
Community Info Conferences & Courses Link to a list of conferences & courses. Find an upcoming conference.  
Community News Links to Candida news postings. Find out about items of interest to the research community.  
Candida Laboratories Links to laboratories who have submitted colleague information to CGD. Find a PI (principal investigator) of a Candida laboratory.  
Candida Community Job Postings Announcements of employment opportunities that are related to Candida biology. View job openings.  
External Links List of useful external sites Find a web site for information not available at CGD.  
Category Resource Description Primary Use Help Page
Submit Data Gene Registry Form to register a gene name. Register a gene name at CGD.  
Gene Naming Guidelines Guidelines for choosing and registering a gene name as agreed upon by the members of the C. albicans community. Find information about registering a gene name and determining when the gene name becomes a standard name.  
Colleague Submission/Update Form Form to submit colleague information to CGD. Your information will be available to CGD users. Add or update your information in CGD.
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Contact CGD Form to submit suggestions or questions to CGD. Send suggestions or questions to CGD.  
Category Resource Description Primary Use Help Page
Download Data Batch Download Tool that allows simultaneous retrieval of DNA sequences, protein sequences, and chromosomal coordinate information for a list of Standard gene names or Feature names. Download information for a list of genes from CGD.
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Gene Ontology (GO) Annotations File The gene_association.cgd file contains the Gene Ontology (GO) curation from CGD. Download tab-delimited files of GO information from CGD.
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Chromosomal Feature Files Tab-delimited files of information about current chromosomal features in CGD. Download feature (gene) names, aliases, descriptions, and other information from CGD.
Sequence Files The sequence download directory contains sequence from the Candida sequencing projects, and derivatives thereof. Download current or archived sequence data.
Phenotypes Tab-delimited files containing the CGD phenotype curation. Download phenotype data.
Orthologs and Best Hits This directory contains the mappings among Candida genes, and between Candida albicans genes and the predicted orthologs or BLAST Best Hits in S. cerevisiae, as well as positional orthologs in C. dubliniensis, plus additional associated information. Download homolog data.
Candida GO Slim Annotations File The GOslim_gene_association.cgd file contains GO Slim annotations for Candida genes, using the CGD GO Slim instead of the entire Gene Ontology. Download tab-delimited files of GO information from CGD.
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Analyses of C. albicans Assembly 21 This directory contains detailed notes about Assembly 21 of the C. albicans genome sequence. The Assembly 21 files were processed at CGD to identify and classify changes that occurred between Assemblies 19, 20, and 21, and to identify other issues, as described in detail on the Sequence documentation page. Download CGD's Assembly 21 analyses.
Analyses of C. albicans Assembly 20 This directory contains detailed notes about Assembly 20 of the C. albicans genome sequence. The Assembly 20 files were processed at CGD to identify and classify changes that occurred between Assembly 19 and Assembly 20, and to identify other issues, as described in detail on the Sequence documentation page. Download CGD's Assembly 20 analyses.
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 and view the SGTC's diagrams of Assembly 19 contigs and their component contigs from Assembly 6.
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 Assembly 6 aliases.
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 Assembly 4 aliases.
Codon Usage Table Table of calculated codon usage frequencies and documentation about how the table was generated. Find codon frequencies for the Candida albicans genome.
Datasets archived at CGD Archive of published and freely available datasets. Download large-scale datasets.  
Category Resource Description Primary Use Help Page
About CGD About CGD About the CGD project. Find out background information on the CGD project.  
CGD Genome Snapshot
C. albicans
C. dubliniensis
C. glabrata
C. parapsilosis
Annotation statistics, updated daily. Find information about the characterization of the genomes in CGD.
Citing CGD How to cite CGD in publications. References to use in citing CGD.  
Staff Names and addresses and CGD staff. Find out who works at CGD.  


A complete list of genes may be found here.
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