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RefSeq: an update on mammalian reference sequences.

Kim D Pruitt1, Garth R Brown, Susan M Hiatt

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.

Nucleic Acids Research
|November 22, 2013
PubMed
Summary
This summary is machine-generated.

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database has expanded its human and mammalian genome annotations. Updates to the eukaryotic annotation pipeline, including RNAseq data, significantly increased transcript and exon discovery.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The NCBI RefSeq database serves as a comprehensive repository for annotated genomic, transcript, and protein sequences.
  • It integrates data from public archives, computational analysis, and expert curation.
  • Maintaining and expanding this database is crucial for biological research.

Purpose of the Study:

  • To report on the growth and recent updates to the mammalian and human subsets of the NCBI RefSeq database.
  • To detail modifications in NCBI's eukaryotic genome annotation pipeline.
  • To describe changes affecting transcript and protein records and annotation policies.

Main Methods:

  • Enhancements to NCBI's eukaryotic genome annotation pipeline for higher throughput.
  • Integration of RNAseq data into the annotation pipeline.
  • Implementation of new policies for reporting supporting evidence, exon feature annotation, and protein annotation for alternatively spliced transcripts.

Main Results:

  • Significant expansion in the number of annotated transcripts and novel exons for mammalian RefSeq genomes.
  • Introduction of structured reports for gene and sequence attributes.
  • Revised protein annotation policy for alternatively spliced transcripts with divergent predicted proteins.

Conclusions:

  • The updated NCBI RefSeq annotation pipeline has improved throughput and significantly expanded the annotation of mammalian and human genomes.
  • Recent changes enhance the reporting of transcript evidence and gene attributes, improving data utility.
  • The RefSeqGene project continues to advance standardized gene and sequence annotation.