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. 2010 Jan;38(Database issue):D428-32.
doi: 10.1093/nar/gkp836. Epub 2009 Oct 6.

New tools at the Candida Genome Database: biochemical pathways and full-text literature search

Marek S Skrzypek  1 , Martha B Arnaud, Maria C Costanzo, Diane O Inglis, Prachi Shah, Gail Binkley, Stuart R Miyasato, Gavin Sherlock
Affiliations

New tools at the Candida Genome Database: biochemical pathways and full-text literature search

Marek S Skrzypek et al. Nucleic Acids Res. 2010 Jan.

Abstract

The Candida Genome Database (CGD, http://www.candidagenome.org/) provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. Herein, we describe two recently added features, Candida Biochemical Pathways and the Textpresso full-text literature search tool. The Biochemical Pathways tool provides visualization of metabolic pathways and analysis tools that facilitate interpretation of experimental data, including results of large-scale experiments, in the context of Candida metabolism. Textpresso for Candida allows searching through the full-text of Candida-specific literature, including clinical and epidemiological studies.

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Figures

Figure 1.
Figure 1.
C. albicans biochemical pathways. Pathways may be viewed at five different levels of detail, and the names of each compound, enzyme and protein are hyperlinked to their respective report pages. (A) Part of the web page report for the tetrahydrofolate biosynthesis pathway, displayed at an intermediate detail level. (B) A fragment of the pathway shown at high detail. (C) The report page for the reaction catalyzed by Dfr1p. (D) The report page for the enzymatic activity of Dfr1p.
Figure 2.
Figure 2.
Textpresso for Candida. (A) Entry of search criteria. An example search for the keywords ‘dectin-1’ and ‘deficient’ is shown. The results were also filtered to show only those articles that contain ‘C. albicans’ in the title. (B) A portion of the output, which is customizable, showing the abstract and matching sentences for an article.
See this image and copyright information in PMC

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