brownbag-science

NCBI Resources

GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains over 6.25 trillion base pairs from over 1.6 billion nucleotide sequences for 450 000 formally described species. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage.

NCBI is a primary steward for biological sequence databases

• RefSeq (Reference Sequence): A collection of curated, non-redundant genomic DNA, transcript (RNA), and protein sequences produced by NCBI.

• GenBank: collection of submitted DNA sequences (Standard Sequences, International Consortium – not NCBI “owned”)

• Gene
• dbGaP: data and results from studies that have investigated the interaction of genotype and phenotype in Humans

• dbSNP

• Clinvar: Clinically relevant variants

Note: each resource usually has its own identifier

Example

Symbol: APRT

Name: adenine phosphoribosyltransferase

Location: Chromosome 16 (88809339..88811928, complement)

	Transcript	Protein
variant 1	NM_000485.3	NP_000476.1
variant 2	NM_001030018.2	NP_001025189.1

Nomenclature

Location

• Genomic (NC) – Chromosome
  • GRCh38
  • GRCh37
• Transcript (NM) – mRNA
• Gene (NG)
• Protein (NP)

Also see: HGVS the standard notation / nomenclature for variants

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