Cited by 458Fungal and yeast genetics researchGenomics and Phylogenetic StudiesYeasts and Rust Fungi Studies

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

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Skrzypek, Marek S., Binkley, Jonathan, Binkley, Gail, Miyasato, Stuart R., Simison, Matt, Sherlock, Gavin·2017·Nucleic Acids Research

DOI 10.1093/nar/gkw924PMC PMC5210628

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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.

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Authors: Skrzypek, M. S., Binkley, J., Binkley, G., Miyasato, S. R., Simison, M., & Sherlock, G.
Affiliations: Stanford Medicine (US)
Corresponding author: Sherlock, Gavin
ORCID: Skrzypek, Marek S.
Miyasato, Stuart R.
Simison, Matt
Sherlock, Gavin
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2016-10-13
Volume: 45
Issue: D1
Pages: D592-D596
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkw924
PMC: PMC5210628
OpenAlex: W2530772399
Cited by: 455
References: 45
Citations by year: 2026: 35 · 2025: 61 · 2024: 68 · 2023: 44 · 2022: 45 · 2021: 69 · 2020: 38 · 2019: 45 · 2018: 39 · 2017: 10 · 2016: 1
FWCI: 16.64
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/4.0/ (vor, 83 d)
Locations: Nucleic Acids Research (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: National Institute of Dental and Craniofacial Research (R01DE015873)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Immunology and Microbiology › Microbiology › Yeasts and Rust Fungi Studies
Keywords: Candida albicans, genome assembly, JBrowse, RNA-seq, genome annotation, fungal genomics
MeSH terms: Candida, Fungal Proteins, Software, Open Reading Frames, Genome, Fungal, Computational Biology, Genomics, Databases, Nucleic Acid, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing, Web Browser

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