Public Sequence Databases
One-Sentence Definition
Public sequence databases are the shared archives and curated resources that store microbial sequences, genomes, annotations, and typing nomenclature for global reuse.
Simple Explanation
Almost every analysis compares your data to someone else’s data. These are the places that data lives.
Detailed Scientific Explanation
| Resource | Content |
|---|---|
| INSDC (NCBI/GenBank, ENA, DDBJ) | Primary archives: SRA/ENA reads, assemblies, annotations |
| RefSeq | Curated non-redundant reference genomes |
| UniProt / Pfam / InterPro | Proteins, families, domains |
| PDB / AlphaFold DB | Experimental and predicted structures (Structural Bioinformatics) |
| PubMLST / Institut Pasteur / EnteroBase / Ridom | Typing schemes and allele nomenclature (MLST and cgMLST) |
| CARD / ResFinder / NCBI AMRFinderPlus (Reference Gene Catalog) | Resistance determinants (AMR Gene Databases) |
| VFDB / BV-BRC | Virulence and integrated pathogen data |
| GTDB / SILVA | Taxonomy and rRNA references (16S Amplicon Analysis) |
| Nextstrain / GISAID | Viral surveillance (Viral Genomics and Surveillance) |
Practical issues: metadata quality is often poor, mislabeled genomes propagate errors, and access terms differ (open archives vs restricted-sharing platforms).
Mechanism
Accessioned records with versioning; programmatic access via APIs (E-utilities, ENA REST) and bulk downloads (datasets, sra-tools).
Clinical Importance
- Comparing a local isolate with global lineages puts a hospital cluster in international context
Research Importance
- Reanalysis and meta-analysis depend on submission compliance
Diagnostic Relevance
- Reference databases define what a diagnostic pipeline can detect
AMR Relevance
- Surveillance networks (WHO GLASS-linked genomic efforts) depend on shared data
Related MOCs
Active Recall Questions
- What is INSDC?
- Which resources define typing nomenclature?
- Why is metadata quality a limiting factor?