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. 2022:2542:55-69.
doi: 10.1007/978-1-0716-2549-1_4.

How to Use the Candida Genome Database

Marek S Skrzypek  1 , Jonathan Binkley  1 , Gavin Sherlock  2
Affiliations

How to Use the Candida Genome Database

Marek S Skrzypek et al. Methods Mol Biol. 2022.

Abstract

The Candida Genome Database provides access to biological information about genes and proteins of several medically important Candida species. The website is organized into easily navigable pages that enable data retrieval and analysis. This chapter shows how to explore the CGD Home page and Locus Summary pages, which are the main access points to the database. It also provides a description of how to use the GO analysis tools, GO Term Finder, and GO Slim Mapper and how to browse large-scale datasets using the JBrowse genome browser. Finally, it shows how to search and retrieve data for user-defined sets of genes using the Advanced Search and Batch Download tools.

Keywords: Candida; Expression analysis; GO Slim; Gene ontology; Genome database; JBrowse.

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Figures

Figure 1
Figure 1
Basic Information section of the of the Summary Tab of the Locus Summary page for C. albicans gene ERG11. The red arrows point to the “search our site” box (a) and the tabs that lead to pages with more detailed information (b). Other sections of the Summary Tab are available by scrolling down.
Figure 2
Figure 2
GO Term Finder query building window. The red arrows point to the pull-down menu for selecting the species (a); the input box where your list of genes is entered (b); and the radio buttons for selecting the GO aspect (c).
Figure 3A
Figure 3A
JBrowse browser window. The display shows a fragment of C. albicans Chromosome 1, Haplotype A. The bars depict transcribed features, color-coded for the + or − strand, and a small arrow indicating the direction of transcription. Several tracks are selected by default. The red oval indicates the navigation tools, and the red arrow next to it points to the “Select tracks” button.
Figure 3B
Figure 3B
JBrowse Select Tracks window (truncated). The main panel shows the available tracks with their Conditions, Techniques and Types. The left panel shows categories that allow filtering the tracks in the main panel. The red arrow points the “Back to browser” button.
Figure 4
Figure 4
Batch Download query building window. The arrows indicate the input box (a); the pull-down menus for species/assembly selection (b); the chromosome/contig/coordinates input boxes (c); and checkboxes for selecting the data type(s) to retrieve (d).
See this image and copyright information in PMC

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