NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

By Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott. Nucleic Acids Res., 2004

3,239 citations recorded by the source corpus.

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b307d55ba07058d6183991d2d2a81b340d558186

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline (2007, methodology): “Sequence databases used in manually directed searches were the ‘microbial’ subset of RefSeq version 19 ( 19 ), and environmental shotgun sequences from acid mine drainage (33) (GenBank accession AADL01000000) and Sargasso Sea (34) (AACY01000000).”
MaGe: a microbial genome annotation system supported by synteny results (2006, methodology): “Second, the complete bacterial proteomes are extracted from the NCBI RefSeq ( 41 ) and EBI Genome Reviews (52) databanks and stored in PkGDB.”
Computing Highly Correlated Positions Using Mutual Information and Graph Theory for G Protein-Coupled Receptors (2009, methodology): “org/7tm/), NCBI’s Refseq database [123,124], the ROOT analysis tool-kit [125], and thank Rene Brun, Fons Rademakers and their development and support team.”
NCBI Viral Genomes Resource (2014, neutral): “ncbi.nlm.nih.gov/genome/viruses/) (10) .”
Using native and syntenically mapped cDNA alignments to improve de novo gene finding (2008, methodology): “The TRANSMAP hints were generated by mapping the BLAT alignments of RefSeq mRNAs ( Pruitt et al. (2007) ) for five organisms obtained from the UCSC genome browser database (Kuhn et al. (2006)).”
Choosing BLAST options for better detection of orthologs as reciprocal best hits (2008, background): “These have been proposed as a source of functional innovation (Francino, 2005; Ohno, 1970 ) and are less expected to have similar functions.”
IMG ER: a system for microbial genome annotation expert review and curation (2009, positive): “IMG ER tools allow addressing annotation problems detected with IMG’s comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function.”
UniPROBE: an online database of protein binding microarray data on protein–DNA interactions (2008, background): “The ﬁrst section (Figure 2A) provides additional annotations for the factor of interest, including unique gene or protein accession numbers (if available as provided by the species-speciﬁc database), gene synonyms, DNA-binding domain amino acid sequence (if available) and links to databases such as ”
GtRNAdb: a database of transfer RNA genes detected in genomic sequence (2008, methodology): “Protein-coding genes annotated in RefSeq (8) were used to compute codon usage of the genome.”
Jetset: selecting the optimal microarray probe set to represent a gene (2011, methodology): “We used NCBI BLASTN to search the 25-base probe sequences for matches to the Refseq human cDNA database [18].”
BlobToolKit – Interactive Quality Assessment of Genome Assemblies (2019, background): “2), which is tagged as the RefSeq (Pruitt et al. 2005) representative genome, each contain 4.3 Mb of sequence assigned to Apicomplexa.”
Entrez Gene: gene-centered information at NCBI (2010, methodology): “Annotation in sequences from NCBI’s Reference sequence project (2) or the International Nucleotide Sequence Database Collaboration (DDBJ, EMBL, GenBank) (3) is integrated with information from collaborating model organism databases, literature review (especially the Gene References into Function or ”