Module 1
2
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2
5
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10
5
From Study material
2-Marks questions
1. Define Bioinformatics.
2. Briefly outline the scope of Bioinformatics.
3. How does the "Central Dogma" of molecular biology serve as the foundation for
bioinformatics analysis?
4. Differentiate between "Sequence Data" and "Structure Data."
5. What is "Expression Data" and why is it unique compared to sequence data?
6. Define a "Primary Database" and provide an example for nucleic acids.
7. What is UniProt, and what are its two main components?
8. Explain the concept of a "Secondary Database."
9. What is the significance of the "InterPro" database?
10. Describe the purpose of the Pfam database.
11. What are "Specialized Databases"? Provide one example.
12. Explain the function of the "Entrez" system at NCBI.
13. What is "EBI Search" (formerly SRS) and how does it facilitate data retrieval?
14. Mention two major differences between NCBI and EBI in terms of data management.
15. Why is the "FASTA" format standard in bioinformatics data retrieval?
5-Marks questions
1. Define Bioinformatics. Explain its interdisciplinary nature and list at least three major
applications.
2. Describe the central dogma of molecular biology. How does bioinformatics support each
stage (DNA → RNA → Protein)?
3. Differentiate between the three main biological data types: Sequence data, Structural
data, and Gene expression data. Provide one example file format for each.
4. GenBank and UniProt are primary databases. Compare their data contents, file formats,
and typical use-cases in bioinformatics pipelines.
5. What are secondary databases? Explain with reference to InterPro and Pfam, highlighting
how they derive information from primary databases.
6. A protein sequence search in Pfam identifies two domains with E-values 3e-12 and 0.004.
Explain what these E-values indicate. Which domain match is more statistically significant
and why?
7. Explain how to retrieve a gene sequence from NCBI using the following tools: NCBI
Nucleotide, BLAST, and ORF Finder. Provide a short workflow diagram or bullet steps.
8. The UniProt entry for a protein contains the following fields: “Sequence length = 431 aa”,
“Mass = 47.9 kDa”, “Isoelectric point = 6.2”. Explain how each of these attributes can be
used in experimental or computational bioinformatics.
9. What is the difference between specialized databases and primary/secondary databases?
Give two examples of specialized databases and describe the type of data contained in
each.
10. A nucleotide sequence contains 380 A/T bases and 120 G/C bases. Calculate the GC
content percentage. Explain the significance of GC-content in sequence analysis.
11. A DNA sequence contains: A = 250, T = 230, G = 180, C = 140
(a) Calculate the GC percentage.
(b) Explain one application of GC-content in genome analysis.
12. A BLASTP search gives the following domain hits:
Domain Bit Score E-value
Pfam-A Domain X 52 4e-10
Pfam-B Domain Y 45 3e-6
Unknown Domain Z 41 0.0008
(a) Arrange the domains in order of statistical significance.
(b) State whether Domain Z should be considered reliable.
13. Given a protein sequence of 85 amino acids, average residue mass = 110 Da, calculate
approx. molecular weight. Discuss why experimental mass may differ from theoretical mass
14. A DNA sequence is:
ATG GCT ACT TGA TAC CTA GAA
Identify: 1) Start codon 2) Stop codon 3) ORF length in nucleotides and amino acids
15. Translate the following mRNA (use standard codon table):
AUG GGU UCU AAU UGA CCA
State 1) Amino acid sequence 2) Where translation stops
16. Given two expression levels:
Control = 200
Treated = 800
Calculate 1) Fold change 2) Log₂ fold change 3) Interpret whether the gene is up/down-
regulated
10-Marks questions
1. Write a detailed note on the scope of bioinformatics, covering:
Genomics, proteomics, transcriptomics
Drug design and molecular docking
Personalized medicine
Systems biology
Biological database & algorithm development
2. Explain the Central Dogma (DNA → RNA → Protein).
Discuss bioinformatics tools used at each stage:
DNA Analysis (FASTQC, BLASTN, Entrez)
RNA Analysis (RNAfold, Salmon, HISAT2)
Protein Analysis (UniProt, Pfam, FoldIndex, SWISS-MODEL)
3. Describe in detail the three major biological data types:
Sequence (nucleotide, protein)
Structure (3D coordinates, PDB)
Expression (microarray, RNA-Seq)
Explain data formats, file structure, analysis pipelines, and computational challenges.
4. Align the following sequences using +1 for match, –1 for mismatch, –2 for gap:
Sequence 1: ATGCA
Sequence 2: ATGGA
Perform global alignment (Needleman–Wunsch) and compute 1) Alignment 2) Total
alignment score
5. A UniProt protein entry shows:
Length = 612 aa
Molecular weight = 67,250 Da
Charge at pH 7 = –12
Isoforms = 3
Two Pfam domains found
Explain numerically 1) Why protein length does not always correlate with MW, 2) How Pfam
computes domain scores 3) How charge prediction tools estimate net charge
6. For two sequences of lengths m = 22 and n = 18, compute 1) Size of the dot-plot matrix 2)
Number of diagonal paths 3) Expected number of random matches if match probability =
0.25
7. Explain with diagrams:
Primary databases: GenBank, DDBJ, EMBL, UniProtKB
Secondary databases: Pfam, InterPro, PROSITE
Specialized databases: Rfam, KEGG, PDBsum, OMIM
Compare how data flow from primary → secondary → specialized.
[Link] step-by-step how to retrieve gene, protein, and literature information using:
NCBI Entrez
BLAST & BLASTP
EBI ENA
UniProt tools
EMBL-EBI search interfaces
Add annotated workflow diagrams (optional).
9. Explain the key algorithms used in sequence comparison:
Dynamic programming (Needleman–Wunsch, Smith–Waterman)
Heuristic methods (BLAST, FASTA)
Profile HMMs (Pfam domain search; Durbin et al.)
Include scoring schemes, matrices, gap penalties, and algorithm complexity.