brownbag-science

NCBI Resources

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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