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

By M. Skrzypek, J. Binkley, G. Binkley, S. Miyasato, Matt Simison, Gavin Sherlock. Nucleic Acids Res., 2016

420 citations recorded by the source corpus.

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.

Subfields: Epidemiology, Food Science, Infectious Diseases

View Paper: https://www.semanticscholar.org/paper/b4e319519353705c0b226f954f6c9ab35596408a

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Citations in the corpus

• The BioGRID interaction database: 2019 update (2018, methodology): “The BioGRID annotation system combines many online resources that include Entrez Gene, UniProt, Ensembl, RefSeq, HGNC, SGD, CGD, MGI, FlyBase, WormBase, TAIR, PubMed and GenBank to aid in this process.”
• VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center (2021, methodology): “Functional annotations have also been integrated or updated from other external databases such as MIPS Functional Catalogue (23), AspGD (24), SGD (25), CGD (26), PomBase (27) and the Neurospora crassa e-Compendium (28) for fungal genomes in addition to providing link outs from other resources such a”
• The BioGRID interaction database: 2017 update (2016, background): “This effort to delineate well-defined, standardized ge-netic interaction (GI) terms has been supported by various MODs, including ZFIN (21), FlyBase (24), SGD (25), CGD (38), PomBase (23) and TAIR (39).”
• The Gene Ontology knowledgebase in 2023 (2023, neutral): “elegans (nematode) 17,171 560 CGD* (Skrzypek et al. 2017) Candida albicans (yeast pathogen) 17,113 0 EcoCyc* (Keseler et al.”