RefSeq: an update on mammalian reference sequences

By Kim D. Pruitt, Garth R. Brown, S. Hiatt, Françoise Thibaud-Nissen, Alex Astashyn, O. Ermolaeva, C. Farrell, Jennifer Hart, M. Landrum, Kelly M. McGarvey and 19 more. 2013

1,002 citations recorded by the source corpus.

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence archives and from computation, curation and collaboration (http://www.ncbi.nlm.nih.gov/refseq/). We report here on growth of the mammalian and human subsets, changes to NCBI’s eukaryotic annotation pipeline and modifications affecting transcript and protein records. Recent changes to NCBI’s eukaryotic genome annotation pipeline provide higher throughput, and the addition of RNAseq data to the pipeline results in a significant expansion of the number of transcripts and novel exons annotated on mammalian RefSeq genomes. Recent annotation changes include reporting supporting evidence for transcript records, modification of exon feature annotation and the addition of a structured report of gene and sequence attributes of biological interest. We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project.

Subfields: Molecular Biology

How researchers see this paper

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

In Molecular Biology

Citations in the corpus

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more (2020, neutral): “For instance, to introduce a cross-reference to UniProt or RefSeq, we have required both exact species and exact sequence matching.”
ClinVar: public archive of relationships among sequence variation and human phenotype (2013, background): “Human Genome Variation Society (HGVS) (4) expressions are reported based on the current reference assembly, RefSeqGenes (5), cDNAs and proteins as appropriate.”
The UCSC Genome Browser database: 2015 update (2014, neutral): “Accompanying the genomes are details of the sequencing and assembly, gene models from RefSeq (3,4), GENCODE (5), Ensembl (6,7) and UCSC (8), transcription evidence from GenBank (9) and other sources, epigenetic and gene regulatory annotation including comprehensive data sets from the ENCODE project ”
The Ensembl gene annotation system (2016, background): “For human, this includes cross-referencing to the HGNC (92), RefSeq (69), UCSC (93), OMIM (94), CCDS, UniProt, ENA and other external databases.”
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) (2016, methodology): “In future, the flexibility of this pipeline will allow integration of additional information from Ensembl to improve functional annotation, for example with all genes within a specified genomic region from both the RefSeq (19) and GENCODE (20) gene sets.”
AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential (2019, methodology): “Reference genomes were obtained from NCBI Refseq (32) in September 2017 and incorporated into a SQL database including taxon metadata.”
In silico prediction of splice-altering single nucleotide variants in the human genome (2014, methodology): “We also used the retrained models to compute ensemble prediction scores for all potential scSNVs across the human genome annotated by either RefSeq database release 62 (23) or Ensembl database release 73 (42).”
The UniProtKB guide to the human proteome (2016, background): “After reexamination and exchanges between resources, this putative protein-coding gene was reconsidered a pseudogene by Havana, HGNC, RefSeq and UniProtKB, and the corresponding record (UniProtKB P0CB46) was deleted from release 2015_10 of UniProt.”
NONCODE 2016: an informative and valuable data source of long non-coding RNAs (2015, methodology): “Although it is reasonable to assume that unannotated transcription is unique to specific lineages, the low RefSeq detection rate was unusual.”
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations (2014, methodology): “We have always considered UniPROTKB SwissProt (9), followed by NCBI RefSeq NP (10), to be the most reliable protein sequence resource.”
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing (2015, methodology): “We also employed A. mellifera gene sequences collected from the National Center for Biotechnology Information Reference Sequence Database (NCBI RefSeq, [47]) as a model to obtain homology-based gene annotation.”
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data (2014, methodology): “We have established a number of collaborations in the field of sequence curation with other groups such as Ensembl (18) and RefSeq (19) and with organism-specific databases to ensure that users are provided with a consistent set of protein sequences across these resources.”
Ensembl 2016 (2015, methodology): “RefSeq transcripts that exactly match an overlapping Ensembl-generated model, with respect to the entire model or just coding exons, are annotated accordingly.”
PHASTER: a better, faster version of the PHAST phage search tool (2016, background): “The latest version of the bacterial sequence database consists of > 16 million protein sequences from RefSeq (17).”
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models (2015, methodology): “Genome annotations for the models were downloaded from the National Center for Biotechnology Information (NCBI) reference sequence database (RefSeq) database (26).”
Ensembl 2022 (2021, background): “Select transcript is a single identical transcript per proteincoding locus that is in both the Ensembl/GENCODE set and NCBI’s RefSeq set (18).”