6.4.2 · HinglishBioinformatics & Computational Biology
Describe biological databases (GenBank, UniProt, PDB)
6.4.2· Biology › Bioinformatics & Computational Biology
Biological databases KYUN exist karte hain?
KYUN (kya problem solve karte hain ye):
- Ek akela sequencing run billions of bases produce kar sakta hai — koi insaan yeh sab aankhon se nahi dekh sakta.
- Discoveries ka koi fayda nahi agar share aur compare na ho sakein. Databases ek common reference dete hain taaki Japan ki lab A aur Brazil ki lab B usi gene ke baare mein baat karein.
- Ye comparison enable karte hain (nai sequence ko BLAST karo jo bhi kabhi deposited hua hai uske against) aur reuse bhi (pehle ke kaam pe build karo, dobara sequence karne ki zaroorat nahi).
Primary vs Secondary databases — dono mein fark samajhte hain:
- Primary (archival): raw experimental submissions as-is store karta hai (GenBank, PDB). Kuch bhi "clean" nahi hota.
- Secondary (curated): primaries se derived processed/annotated knowledge (UniProt/Swiss-Prot). Humans function add karte hain, quality checks bhi.
Teen databases
1. GenBank — nucleotide sequences
- KYA hold karta hai: raw submitted DNA/RNA sequences + metadata.
- KAISE access karein: NCBI ke through; search tool = Entrez; similarity search tool = BLAST (Basic Local Alignment Search Tool).
- ID example: accession jaise
NM_000518(human beta-globin mRNA). - Format: FASTA (sirf sequence) ya GenBank flat-file (sequence + rich annotation).
2. UniProt — protein sequences & function
- KYA hold karta hai: protein sequence + function, domains, PTMs, subcellular location, disease links, cross-references.
- Curation kyun matter karta hai: ek quality vs coverage trade-off ke liye do databases hain — Swiss-Prot chhota hai par trustworthy; TrEMBL bahut bada hai par tentative.
- ID example: accession
P68871(human hemoglobin subunit beta).
3. PDB — 3D structures
- KYA hold karta hai: har atom ke atomic (x, y, z) coordinates, plus jo method use hua.
- Structures kaise solve hoti hain: X-ray crystallography, NMR spectroscopy, cryo-EM.
- ID example: ek 4-character code jaise
1HHO(human oxyhemoglobin). (Yeh 4-char ID exam mein classic giveaway hai.) - File formats: legacy
.pdb, modern.cif(mmCIF), jo bahut badi structures handle karta hai. - Quality metric: resolution Ångströms (Å) mein — lower is better: 1.5 Å sharp hai, 3.5 Å blurry hai.
Ye kaise connect hote hain (central dogma view)
| Feature | GenBank | UniProt | PDB |
|---|---|---|---|
| Data type | Nucleotide (DNA/RNA) | Protein sequence + function | 3D atomic structure |
| Class | Primary | Secondary (curated) + auto | Primary |
| Managed by | NCBI (INSDC) | UniProt Consortium | wwPDB |
| Search/tool | Entrez, BLAST | UniProt search, BLAST | RCSB search |
| ID example | NM_000518 | P68871 | 1HHO |
| Key metric/split | annotation | Swiss-Prot / TrEMBL | resolution (Å) |
Worked reasoning examples
Active Recall
Recall Dhako aur khud test karo
- Kaunsa DB DNA/RNA store karta hai? → GenBank
- Kaunsa DB 3D coordinates store karta hai? → PDB
- Kaunsa DB curated protein resource hai? → UniProt
- GenBank ke do international partners? → ENA (Europe), DDBJ (Japan)
- UniProt reviewed vs unreviewed? → Swiss-Prot (manual) vs TrEMBL (auto)
- Resolution (Å) mein lower better hai ya higher? → Lower Å = better
- PDB ID format? → 4 characters (e.g., 1HHO)
- Primary vs secondary database? → primary = raw archive; secondary = curated/derived
Recall Feynman: 12-saal ke bachhe ko samjhao
Socho teen badi online libraries hain. Pehli (GenBank) genes ki spelling rakhti hai — A, T, G, C letters. Doosri (UniProt) proteins kya kaam karti hain yeh rakhti hai — jaise har protein ki job description. Teesri (PDB) proteins ke 3D LEGO models rakhti hai jo dikhate hain protein fold hone ke baad kaisi dikhti hai. Duniya bhar ke scientists apni findings in libraries mein daalte hain taaki kisiko zero se shuru na karna pade — aur yeh libraries linked hain, toh ek click mein gene ki spelling se uski job tak, aur uski shape tak pahunch sakte ho.
Flashcards
GenBank kis type ka data store karta hai?
Nucleotide (DNA/RNA) sequences with annotations.
GenBank ko kaun maintain karta hai?
NCBI (NIH ka part), INSDC collaboration ke andar.
GenBank ke international partner databases kaunse hain?
ENA (Europe) aur DDBJ (Japan).
GenBank mein similar sequences search karne ka tool?
BLAST (Basic Local Alignment Search Tool).
UniProt kis type ka data store karta hai?
Protein sequences plus functional annotation.
UniProtKB ke do subsets kaunse hain?
Swiss-Prot (manually curated) aur TrEMBL (auto-annotated).
Kaunsa UniProt subset manually reviewed hai?
Swiss-Prot.
PDB kis type ka data store karta hai?
Experimentally determined 3D atomic structures (coordinates).
PDB mein structures determine karne ke teen methods?
X-ray crystallography, NMR, cryo-EM.
PDB identifier format kya hota hai?
Ek 4-character code (e.g., 1HHO).
Crystallography mein lower ya higher resolution better hoti hai?
Lower Å value = better (finer detail).
Primary vs secondary database kya hota hai?
Primary = raw archival submissions (GenBank, PDB); secondary = curated/derived (Swiss-Prot).
PDB ko kaunsa consortium manage karta hai?
wwPDB (RCSB, PDBe, PDBj).
Teen databases ka central-dogma mapping?
DNA→GenBank, protein sequence→UniProt, 3D structure→PDB.
Badi structures ke liye modern PDB file format?
mmCIF (.cif).
Connections
- Central Dogma of Molecular Biology — DNA→protein→structure logic jo har DB capture karta hai
- Sequence Alignment & BLAST — woh tool jo GenBank/UniProt ko searchable banata hai
- Protein Structure Determination — PDB ke peeche X-ray, NMR, cryo-EM
- FASTA and File Formats — sequences kaise store hoti hain
- Protein Folding — kyun 3D structure (PDB) sequence (UniProt) se alag hoti hai
- Genome Annotation — GenBank raw sequence ko UniProt function mein convert karna