RefSeq

Identifier

refseq

License

Public domain

Citation

O'Leary NA, et al. Reference sequence (RefSeq) database at NCBI. Nucleic Acids Res 2016;44(D1):D733-D745. doi:10.1093/nar/gkv1189

Overview

RefSeq genome-assembly metadata, sequences, and annotations from NCBI Genomes FTP assembly packages.

assembly_summary combines current and historical master summaries without filtering by version status or RefSeq exclusion.

It provides the assembly identifiers and package URLs used by the assembly-specific tables.

Tables

• refseq.alignments — Explicit RefSeq sequence-to-assembly alignment blocks from genomic GFF3 rows.
• refseq.assembly_regions — Genomic regions with alternate-scaffold and patch placements from assembly-specific *_assembly_regions.txt reports when NCBI supplies one.
• refseq.assembly_sequences — Sequence records from RefSeq assembly reports.
• refseq.assembly_statistics — Assembly statistics from assembly-specific *_assembly_stats.txt reports.
• refseq.assembly_summary — Current and historical RefSeq genome assemblies from NCBI master summary files, one row per assembly.

assembly_name is NCBI’s human-readable asm_name label and may not be globally unique.

• refseq.cds — RefSeq coding-sequence (CDS) intervals derived from explicit CDS rows in genomic GFF3 files.
• refseq.exons — RefSeq exon intervals derived from explicit exon rows in genomic GFF3 files.
• refseq.gene_segments — RefSeq immunoglobulin and T-cell-receptor gene-segment intervals from explicit genomic GFF3 rows.
• refseq.genes — RefSeq gene and pseudogene annotations derived from genomic GFF3 files.
• refseq.genome_nucleotides — Individual nucleotide positions from assembly-specific *_genomic.fna.gz files.
• refseq.genomic_gaps — Gap intervals in top-level RefSeq genomic sequences from assembly-specific *_genomic_gaps.txt.gz reports when NCBI supplies one.
• refseq.protein_amino_acids — Individual amino-acid positions from assembly-specific *_protein.faa.gz files.
• refseq.recombination_features — RefSeq recombination intervals from explicit genomic GFF3 rows.
• refseq.regulatory_features — RefSeq regulatory-element intervals from explicit genomic GFF3 rows. regulatory_type preserves the source class while the shared schema retains element-specific annotations.
• refseq.repeat_features — RefSeq repeat intervals from explicit genomic GFF3 rows. repeat_type preserves the source class, while the repeat-unit and mobile-element qualifiers describe repeat subclasses when supplied.
• refseq.replication_features — RefSeq DNA-replication intervals from explicit genomic GFF3 rows. replication_type preserves the source class while the shared fields retain its evidence and functional annotations.
• refseq.rna_nucleotides — Individual nucleotide positions from assembly-specific *_rna.fna.gz files.
• refseq.sequence_alterations — RefSeq sequence-change and assembly-artifact intervals from explicit genomic GFF3 rows.
• refseq.sequence_annotations — RefSeq sequence-level annotations from explicit genomic GFF3 rows. annotation_type preserves the source type; the table name avoids ambiguity with the literal sequence_feature source type.
• refseq.sequence_regions — RefSeq sequence-level metadata and rare region-form repeat annotations from explicit genomic GFF3 region rows.
• refseq.structural_features — RefSeq structural sequence-element intervals from explicit genomic GFF3 rows.
• refseq.transcripts — RefSeq RNA and transcript annotations from genomic GFF3 files. transcript_type preserves the source class.