2 Biological Databases and Data Retrieval Free Online FlashCards

Which three archives collaborate through INSDC?

INSDC links GenBank, the European Nucleotide Archive (ENA), and the DNA Data Bank of Japan (DDBJ), which exchange and synchronize submitted nucleotide records.

How does RefSeq differ from archival nucleotide databases?

RefSeq is a non-redundant collection of reference sequences drawn from public data, with varying levels of validation and curation. Its prefixes indicate record type and status conventions, not guaranteed experimental confirmation.

Where are raw sequencing reads commonly archived?

The Sequence Read Archive (SRA) commonly stores raw sequencing reads; assembled or annotated nucleotide sequences are found in resources such as GenBank and ENA.

How do Swiss-Prot and TrEMBL differ?

Swiss-Prot is manually reviewed; TrEMBL is computationally annotated and is not manually reviewed in the same way.

Which UniProtKB identifier should you use when citing an entry?

Use the UniProt accession as the stable identifier when citing an entry; the mnemonic entry name is useful but is not the preferred stable identifier.

What is the difference between a PDB entry identifier and a chain identifier?

A PDB entry identifier refers to a deposited structure record, while chain identifiers distinguish molecular instances within that record.

What do `map00010` and `hsa00010` identify in KEGG?

`map00010` identifies a reference glycolysis/gluconeogenesis map; `hsa00010` identifies the human organism-specific map.

Does a pathway record prove its reactions are active in a sample?

A pathway record represents organized biological knowledge; it does not directly measure whether every listed reaction is active in a particular sample.

What does a sequence accession’s version suffix specify?

The accession identifies the record, while the version suffix identifies a particular sequence version. The sequence can change between versions even if the accession remains the same.

When should you choose FASTA rather than a flat-file or XML record?

FASTA is convenient for sequence-only tasks. A flat-file or XML record preserves more annotation and provenance.

Why should a database identifier be recorded with its database and record type?

Interpret an identifier together with its database and record type. A human-readable gene symbol can be ambiguous, species-dependent, or revised.

What should you verify after finding a biological database record?

Verify the organism, sequence or entity, accession version, annotation status, evidence, and links to related records.