NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

By Kim D. Pruitt, Tatiana A. Tatusova, Garth R. Brown, Donna R. Maglott. Nucleic Acids Res., 2011

1,184 citations recorded by the source corpus.

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records. These records are selected and curated from public sequence archives and represent a significant reduction in redundancy compared to the volume of data archived by the International Nucleotide Sequence Database Collaboration. The database includes over 16 000 organisms, 2.4 × 106 genomic records, 13 × 106 proteins and 2 × 106 RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links to related sources of information. We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline. More information about the resource is available online (see http://www.ncbi.nlm.nih.gov/RefSeq/).

Subfields: Molecular Biology

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Citations in the corpus

MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins (2015, background): “0 database is based on human and mouse RefSeq proteins (release 63) (16) that are mapped to NCBI Gene loci (ftp.”
NONCODEv4: exploring the world of long non-coding RNA genes (2013, methodology): “In total, 118 148, 141 194 and 35 445 transcripts were retrieved from literature, Ensembl and RefSeq, respectively.”
Predicting effective microRNA target sites in mammalian mRNAs (2015, neutral): “20.1 (parameters ‘-s -name -tab ’) ( Quinlan and Hall, 2010 ).”
Ensembl 2013 (2012, background): “For example, we provide up to date external database references to gene names from the HUGO Gene Nomenclature Committee (HGNC) (1), the Universal Protein Resource (UniProt) (2), Orphanet portal for rare diseases and orphan drugs (3), the Online Mendelian Inheritance in Man (OMIM) database (4), the R”
Identification of a large set of rare complete human knockouts (2015, neutral): “Completely knocked-out genesa 1,171 (775) 20 (15) 68 (46)”
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome (2016, methodology): “First we developed a set of reference gene structures by augmenting the TAIR10 dataset with 635 novel gene models from the NCBI RefSeq Gnomon pipeline (Pruitt et al., 2012), the MAKER-P pipeline (Campbell et al.”
Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics (2013, methodology): “In addition to the transcript sequences, we obtained 1,433,269 protein sequences deposited in the plant division of UniProt release 2011_06 (UniProt Consortium 2012) and RefSeq release 47 (Pruitt et al. 2012).”
Rfam 11.0: 10 years of RNA families (2012, background): “The NCBI Reference Sequence collection (RefSeq) is a non-redundant set of annotated sequences (14).”
NCBI Viral Genomes Resource (2014, neutral): “The RefSeq data model for most organisms underscores the importance of very well annotated reference sequence records (26).”
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms (2013, methodology): “The set of transcripts used in this experiment were the curated RefSeq [9] genes (accession prefix NM) from hg18.”
Kraken: ultrafast metagenomic sequence classification using exact alignments (2014, background): “but the library can be customized as needed by individual users [18].”
The Transporter Classification Database (TCDB): recent advances (2015, background): “conserved domains KEGG (31) & BioCyc (32) These resources allow transport systems to be linked with metabolomics data EggNOG (33) Multiple alignments and phylogenetic trees containing a protein of interest can be viewed RefSeq (34) Information about a gene source is provided with comments and refere”
Computational meta'omics for microbial community studies (2013, methodology): “…reads) to functional categories by means of orthology relations with sequences in well-characterized functional databases, such as NCBI nr (Pruitt et al , 2012), the KEGG Orthology (Kanehisa and Goto, 2000), and COGs (Tatusov et al , 1997), or by identifying speciﬁc PFAM (Punta et al ,…”