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NCBI RefSeq: reference sequence standards through 25 years of curation and annotation

Goldfarb, Tamara, Kodali, Vamsi K, Pujar, Shashikant, Brover, Vyacheslav, Robbertse, Barbara, Farrell, Catherine M, Oh, Dong-Ha, Astashyn, Alexander, Ermolaeva, Olga, Haddad, Diana, Hlavina, Wratko, Hoffman, Jinna, Jackson, John D, Joardar, Vinita S, Kristensen, David, Masterson, Patrick, McGarvey, Kelly M, McVeigh, Richard, Mozes, Eyal, Murphy, Michael R, Schafer, Susan S, Souvorov, Alexander, Spurrier, Brett, Strope, Pooja K, Sun, Hanzhen, Vatsan, Anjana R, Wallin, Craig, Webb, David, Brister, J Rodney, Hatcher, Eneida, Kimchi, Avi, Klimke, William, Marchler-Bauer, Aron, Pruitt, Kim D, Thibaud-Nissen, Françoise, Murphy, Terence D·2025·Nucleic Acids Research
DOI 10.1093/nar/gkae1038
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Abstract

Reference sequences and annotations serve as the foundation for many lines of research today, from organism and sequence identification to providing a core description of the genes, transcripts and proteins found in an organism's genome. Interpretation of data including transcriptomics, proteomics, sequence variation and comparative analyses based on reference gene annotations informs our understanding of gene function and possible disease mechanisms, leading to new biomedical discoveries. The Reference Sequence (RefSeq) resource created at the National Center for Biotechnology Information (NCBI) leverages both automatic processes and expert curation to create a robust set of reference sequences of genomic, transcript and protein data spanning the tree of life. RefSeq continues to refine its annotation and quality control processes and utilize better quality genomes resulting from advances in sequencing technologies as well as RNA-Seq data to produce high-quality annotated genomes, ortholog predictions across more organisms and other products that are easily accessible through multiple NCBI resources. This report summarizes the current status of the eukaryotic, prokaryotic and viral RefSeq resources, with a focus on eukaryotic annotation, the increase in taxonomic representation and the effect it will have on comparative genomics. The RefSeq resource is publicly accessible at https://www.ncbi.nlm.nih.gov/refseq.

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Metadata

Authors
Goldfarb, T., Kodali, V. K., Pujar, S., Brover, V., Robbertse, B., Farrell, C. M., Oh, D.-H., Astashyn, A., Ermolaeva, O., Haddad, D., Hlavina, W., Hoffman, J., Jackson, J. D., Joardar, V. S., Kristensen, D., Masterson, P., McGarvey, K. M., McVeigh, R., Mozes, E., Murphy, M. R., Schafer, S. S., Souvorov, A., Spurrier, B., Strope, P. K., Sun, H., Vatsan, A. R., Wallin, C., Webb, D., Brister, J. R., Hatcher, E., Kimchi, A., Klimke, W., Marchler-Bauer, A., Pruitt, K. D., Thibaud-Nissen, F., & Murphy, T. D.
Affiliations
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , 45 Center Drive,  Bethesda , MD 20894 ,
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2024-11-11
Volume
53
Issue
D1
Pages
D243-D257
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gkae1038
Cited by
455
References
8
Language
en
Funders
  • National Center for Biotechnology Information
  • National Library of Medicine
  • National Institutes of Health

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