RefSeq microbial genomes database: new representation and annotation strategy

By Tatiana A. Tatusova, S. Ciufo, B. Fedorov, Kathleen O'Neill, I. Tolstoy. Nucleic Acids Res., 2013

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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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9708363c9191db90c2af98b0d82ae18121a833cb

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Citations in the corpus

RefSeq: an update on prokaryotic genome annotation and curation (2017, background): “…of bacterial genome assemblies, RefSeq in 2013 introduced a set of non-redundant D852 Nucleic Acids Research, 2018, Vol. 46, Database issue protein sequences, each with a single name and each potentially representing a large number of identical protein sequences encoded by many genomes (4).”
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015, methodology): “The workflow starts by collecting genomes from public databases (19,23–26).”
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. (2016, background): “We have recently added three new categories with two-letter codes: “pg” for plasmid genes taken from the RefSeq plasmid section excluding those already represented in the KEGG complete genomes, “vg” for viral genes taken from the RefSeq viral section and “ag” for the internally developed and publica”
Gene: a gene-centered information resource at NCBI (2014, methodology): “The RefSeq project is now defining reference and representative genomes to use as a standard baseline for comparison while continuing to provide genome annotation for all bacterial strains, including disease outbreak isolates, to support surveillance and testing needs (19).”
Circlator: automated circularization of genome assemblies using long sequencing reads (2015, methodology): “By default each contig is searched against the nucleotide sequences of 162 dnaA genes obtained from RefSeq [25] (see Additional file 1 for details).”
Expanded microbial genome coverage and improved protein family annotation in the COG database (2014, methodology): “Each gene entry in a COG is now denoted by its gene index (gi) number in the NCBI protein database and is linked to the respective entry in the NCBI’s RefSeq database (28) which provides links to the nucleotide sequence of the encoding gene in GenBank (29), its chromosomal location in Entrez Gene (3”
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, background): “For example, of the 24,000 bacterial genomes currently in NCBI RefSeq [80], only 55% have associated SRA read data and analysis of the remaining 45% requires genome-based methods.”
Evaluating the Information Content of Shallow Shotgun Metagenomics (2018, methodology): “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.”
NCBI prokaryotic genome annotation pipeline (2016, unknown): “Of note, RefSeq rules include comparative analysis of all genomes in a clade (33).”