Universal Science College

(B. Sc. Biochemistry)

Fourth Semester 2005
Internal Examination Full Marks: 100
Subject: Biochem 225 (Bioinformatics) Pass Marks: 45
Date: July 30, 2005 Time: 3 hours
Candidates are required to give their answers in their own words as far as practicable. The figure in the
margin indicates full marks.
Group (A) Long Questions (Any three) ×14 = 42)
(3×

1. Apply the Needleman-Wunsch Algorithm to determine the best alignment for the following amino acid
sequences. Use a BLOSUM matrix for your match scores and a gap penalty of 8.
Sequence # 1: TVVTGRVE
Sequence # 2 TVATRIE
* Matrix chart attached (BLOSUM 45)
2. Two sequences A and B show significant similarity in a BLAST search. It is known that sequence B is
homologous to sequence C. Which additional information would you require to conclude that sequence
A is homologous to sequence C.
3. What parameters will you use to construct a phylogenetic tree (distance method). Discuss at least for 5
sequences. (Mathematical modulation necessary).
4. Imagine two matrices (PAM 250 and BLOSUM 62). If you want to compare any two protein sequences.
Discuss the role of both the matrices while aligning both protein sequences.

Group (B) Short Questions: (Any six) ×7 = 42)

(6×
1. Differentiate between structural and functional genomics.
2. What is the purpose for gene prediction? Discuss.
3. BLAST and FASTA are two widely used tools for sequence alignment. What are the similarities and
difference in their approaches?
4. What problems are confronted in phylogenetic analysis? Discuss the ways to test phylogenics.
5. Structural protein domains with the same or similar function always show significant similarity. Is this
true of false? Discuss.
6. What is the purpose or gene prediction? Comment.
7. How can you find ORFs in a given DNA sequences. Discuss.
8. What is homology or comparative modeling? Discuss.

Group (C) Write short notes on: (Any eight) ×8 = 16)

(2×

1. What is internet?
2. What is Phrap?
3. What is contig?
4. What is secondary databases?
5. What is file format?
6. What is Entrez?
7. What is algorithm?
8. What is annotation?
9. Define Gene Bank.
10. What is RMSD?
11. Mention few Molecular graphic packages.
12. What is OMIM?
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