The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
RefSeq microbial genomes database: new representation and annotation strategy
Open accessAbstract
The source of the microbial genomic sequences in the RefSeq collection is the set of primary sequence records submitted to the International Nucleotide Sequence Database public archives. These can be accessed through the Entrez search and retrieval system at http://www.ncbi.nlm.nih.gov/genome. Next-generation sequencing has enabled researchers to perform genomic sequencing at rates that were unimaginable in the past. Microbial genomes can now be sequenced in a matter of hours, which has led to a significant increase in the number of assembled genomes deposited in the public archives. This huge increase in DNA sequence data presents new challenges for the annotation, analysis and visualization bioinformatics tools. New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks.
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Cites
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
Pruitt, K. D., Tatusova, T., Brown, G. R., & Maglott, D. R. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1079 · Cited by 1,149 · cited 1×
“The source of the microbial genomic sequences in the RefSeq collection (4) is the set of primary sequence records submitted to the International Nucleotide Sequence Database public archives.”
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Cited by
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0012-7 · Cited by 1,882
Wu, H., Esteve, E., Tremaroli, V., Khan, M. T., Caesar, R., Mannerås-Holm, L., Ståhlman, M., Olsson, L. M., Serino, M., Planas-Fèlix, M., et al. (2017) · Nature Medicine · doi:10.1038/nm.4345 · Cited by 1,632
Gene: a gene-centered information resource at NCBI
Brown, G. R., Hem, V., Katz, K. S., Ovetsky, M., Wallin, C., Ermolaeva, O., Tolstoy, I., Tatusova, T., Pruitt, K. D., Maglott, D. R., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1055 · Cited by 699
Self-citationEvaluating the Information Content of Shallow Shotgun Metagenomics
Hillmann, B., Al-Ghalith, G. A., Shields-Cutler, R. R., Zhu, Q., Gohl, D. M., Beckman, K. B., Knight, R., & Knights, D. (2018) · mSystems · doi:10.1128/msystems.00069-18 · Cited by 474
“Functional profiling was obtained using KEGG Orthology group (KO) (16) annotations for RefSeq-derived genes (20) from directly observed exhaustive gapped alignments in ultradeep WMS sequencing.”
MethodInfluentialHaak, B. W., Littmann, E. R., Chaubard, J.-L., Pickard, A. J., Fontana, E., Adhi, F., Gyaltshen, Y., Ling, L., Morjaria, S. M., Peled, J. U., et al. (2018) · Blood · doi:10.1182/blood-2018-01-828996 · Cited by 273
Metadata
- Authors
- Tatusova, T., Ciufo, S., Fedorov, B., O’Neill, K., & Tolstoy, I.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-12-06
- Volume
- 42
- Issue
- D1
- Pages
- D553-D559
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2120172561
- Cited by
- 483
- References
- 3
- FWCI
- 21.38
- Type
- journal article
- Language
- en
- Open access
- gold
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- Tatusova, T., Ciufo, S., Fedorov, B., O’Neill, K., & Tolstoy, I. (2014). RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Research. https://doi.org/10.1093/nar/gkt1274
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
