Question

An example of primary database is:
(A). GenBank
(B). EMBL
(C). DDBJ
(D). PDB
Choose the correct answer from the options given below:

• A. (A), (B) and (D) only.
• B. (A), (B) and (D) only.
• C. (A), (B), (D) and (C).
• D. (A), (B), (C) and (D).

Hint:

Remember the "Big Four" primary databases: The three INSDC partners (GenBank, ENA, DDBJ) for nucleotide sequences, and the PDB for 3D structures. If data comes directly from an experiment and is just archived, it's a primary database.

Answer 1

The Correct Option is D

Step 1: Understanding the Concept:
In bioinformatics, databases are classified based on the source and nature of their data.
Primary Databases (Archival Databases): These databases store original, raw data submitted directly by researchers. The data is experimentally determined (e.g., nucleotide sequences, protein sequences, protein structures). The database curators perform quality control but do not add further interpretation or annotation.
Secondary Databases (Derived Databases): These databases contain curated information derived from the analysis of primary data. They add value through expert annotation, classification into families, etc. Examples include UniProtKB/Swiss-Prot, Pfam, and InterPro.
The question asks to identify which of the listed databases are primary.
Step 2: Detailed Explanation:
(A) GenBank: This is a primary, archival database of nucleotide sequences, run by NCBI. Researchers submit their raw sequence data here.
(B) EMBL (now ENA - European Nucleotide Archive): This is the European counterpart to GenBank and is also a primary, archival database for nucleotide sequences.
(C) DDBJ (DNA Data Bank of Japan): This is the Japanese counterpart and the third member of the INSDC. It is also a primary, archival nucleotide sequence database.
(D) PDB (Protein Data Bank): This is the worldwide primary, archival database for the 3D structural data of biological macromolecules (proteins and nucleic acids), determined experimentally by methods like X-ray crystallography and NMR spectroscopy.
All four databases listed are repositories of original, experimentally determined data submitted by the scientific community. Therefore, all four are considered primary databases.
Step 3: Final Answer:
GenBank, EMBL (ENA), DDBJ, and PDB are all examples of primary databases. Therefore, option (4) is correct. Note that options 2 and 3 in the OCR are identical to option 4, but 4 is the most complete representation.