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Nucleic Acids Res. 2017 Jan 4;45(D1):D592-D596. doi: 10.1093/nar/gkw924. Epub 2016 Oct 13.

The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data.

Author information

1
Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA.
2
Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA gsherloc@stanford.edu.

Abstract

The Candida Genome Database (CGD, http://www.candidagenome.org/) is a freely available online resource that provides gene, protein and sequence information for multiple Candida species, along with web-based tools for accessing, analyzing and exploring these data. The mission of CGD is to facilitate and accelerate research into Candida pathogenesis and biology, by curating the scientific literature in real time, and connecting literature-derived annotations to the latest version of the genomic sequence and its annotations. Here, we report the incorporation into CGD of Assembly 22, the first chromosome-level, phased diploid assembly of the C. albicans genome, coupled with improvements that we have made to the assembly using additional available sequence data. We also report the creation of systematic identifiers for C. albicans genes and sequence features using a system similar to that adopted by the yeast community over two decades ago. Finally, we describe the incorporation of JBrowse into CGD, which allows online browsing of mapped high throughput sequencing data, and its implementation for several RNA-Seq data sets, as well as the whole genome sequencing data that was used in the construction of Assembly 22.

PMID:
27738138
PMCID:
PMC5210628
DOI:
10.1093/nar/gkw924
[Indexed for MEDLINE]
Free PMC Article

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