NCBI reference sequences

NCBI reference sequences provide a curated, non-redundant collection of genomic, transcript, and protein reference records selected from public sequence archives with structured annotations for genome annotation, comparative genomics, and variant analysis.

Key Features:

• Non-redundant reference set: Records are selected from public sequence archives to produce an integrated, non-redundant collection of genomic, transcript, and protein sequences.
• Extensive taxonomic coverage: The collection covers sequences from over 55,000 organisms, including more than 4,800 viruses, ~40,000 prokaryotes, and ~10,000 eukaryotes.
• Curated annotations: Annotations include coding regions, conserved domains, tRNAs, sequence-tagged sites (STS), variations, literature references, gene and protein product names, and cross-references to other databases.
• Annotation methods: Annotations are produced through automated analyses, prediction algorithms, propagation from GenBank, and manual curation by NCBI staff.
• Quality assurance: Records undergo format checks and quality tests for sequence and annotation accuracy.
• Prokaryotic Genome Annotation Pipeline (PGAP): PGAP combines alignment-based methods with ab initio gene predictions for prokaryotic genome annotation.
• Viral genomics resource: The NCBI Viral Genomes Resource catalogs and curates reference viral genome sequences and leverages community knowledge for well-annotated viral reference sets.
• Taxonomic validation and expansion: Ongoing taxonomic validation and expansion support genome annotation, comparative genomics, and clinical testing applications.

Scientific Applications:

• Genome annotation: Provides stable reference sequences and annotations for annotating genomes across diverse organisms.
• Gene identification and characterization: Supplies curated sequences and feature annotations to support discovery and functional characterization of genes.
• Mutation and polymorphism analysis: Enables identification and interpretation of genetic variations against reference sequences.
• Expression studies: Supports analysis of transcript-level data and gene expression by providing transcript reference sequences and annotations.
• Comparative genomics: Facilitates comparative analyses to assess evolutionary relationships and functional conservation across taxa.
• Viral genome reference curation: Provides curated viral reference genomes to support viral genomics and related analyses.

Methodology:

Records are selected from public sequence archives and processed using automated analyses, prediction algorithms, propagation from GenBank, manual curation by NCBI staff, format checks and quality tests, alignment-based methods and ab initio gene predictions (as implemented in PGAP), and taxonomic validation.