NCBI Reference Sequences: current status, policy and new initiatives

By Kim D. Pruitt, Tatiana A. Tatusova, W. Klimke, Donna R. Maglott. Nucleic Acids Res., 2008

811 citations recorded by the source corpus.

NCBI's Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. RefSeq records integrate information from multiple sources and represent a current description of the sequence, the gene and sequence features. The database includes over 5300 organisms spanning prokaryotes, eukaryotes and viruses, with records for more than 5.5 × 106 proteins (RefSeq release 30). Feature annotation is applied by a combination of curation, collaboration, propagation from other sources and computation. We report here on the recent growth of the database, recent changes to feature annotations and record types for eukaryotic (primarily vertebrate) species and policies regarding species inclusion and genome annotation. In addition, we introduce RefSeqGene, a new initiative to support reporting variation data on a stable genomic coordinate system.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a131f2b33153a7ceaba0b1c3cc34c471536f565c

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Citations in the corpus

Improving RNA-Seq expression estimates by correcting for fragment bias (2011, methodology): “For all human data-sets, the RefSeq refGene annotation for assembly NCBI36/hg18 [30] was used, and was downloaded from the UCSC Genome Browser.”
Computational prediction of secondary and supersecondary structures. (2013, background): “5 million nonredundant protein sequences in the RefSeq database (5), and the fact that experimental determination of protein structure is relatively expensive and time-consuming and cannot keep up with the rapid accumulation of the sequence data (6-9).”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, methodology): “Fully sequenced genomes in STRING are imported from RefSeq (45) and Ensembl (46), as well as from a number of dedicated sites, and are hand-screened for completeness and non-redundancy.”
UniProt Knowledgebase: a hub of integrated protein data (2011, background): “A similar pipeline to import novel sequences from RefSeq is currently being established.”
NONCODE v3.0: integrative annotation of long noncoding RNAs (2011, neutral): “0 (22), RefSeq (23), UCSC (24) and Ensembl (25).”
Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, background): “UniProt, RefSeq (97), IPI (98), gi (99), Entrez (100)) or by keyword suggestions (e.”
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome (2011, methodology): “Two mouse reference transcript sets were used: the RefSeq annotation [34] and the Ensembl annotation [27] (see Methods).”
Database resources of the National Center for Biotechnology Information (2009, neutral): “The NCBI RefSeq database (27) is a nonredundant set of curated and computationally derived sequences for transcripts, proteins and genomic regions.”
The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine (2013, neutral): “Provision of genomic reference sequences based on the NCBI RefSeqGene project (Pruitt et al. 2009), links to available protein structures and homology models, and mapping HGMD phenotypes to the Human Phenotype Ontology (HPO) are also regarded as priorities.”
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium (2009, neutral): “Previously, for genes only identifiers from NCBI Entrez Gene (17) or FlyBase (15) were supported; for proteins only RefSeq (24) or FlyBase identifiers.”
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee (2012, methodology): “Typical homology extension involves performing BLAST or PSI-BLAST [10] against the NR database [11].”
KEGG for representation and analysis of molecular networks involving diseases and drugs (2009, background): “(1) Gene information for completely sequenced genomes is computationally generated from RefSeq (7) and other public resources, and stored in the KEGG GENES database.”
Database resources of the National Center for Biotechnology Information (2011, background): “org), RefSeqGene provides stable, standard human genomic sequences annotated with standard mRNAs for well-characterized human genes (6).”
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction (2012, methodology): “If available, a RefSeq accession is recommended as it carries more information about the sequence [15], which allows Primer-BLAST to better identify the template and thus perform better primer specificity checking.”