BIOTECHNOLOGY

CATEGORY L T P CREDIT
BTT302 BIOINFORMATICS
PCC 2 0 2 4

Preamble:Introduction to computers and Bioinformatics, Basic concepts of biomolecules,

Types of Nucleotide Sequence and DNA sequencing methods, Bioinformatics Resources,
Sequence databases, Sequence file formats, Sequence Analysis, Sequence alignment.

Prerequisite: Basic knowledge in molecular biology, internet basics

Course Outcomes: After the completion of the course the student will be able to

CO 1 Differentiate various biological databases.

CO 2 Infer the terminologies and concepts in the field.
CO 3 Generate and interpret the sequence alignment and implement the scoring
matrices.
CO 4 Articulate the different bioinformatics tools.

Mapping of course outcomes with program outcomes

PO 1 PO 2 PO 3 PO 4 PO 5 PO 6 PO 7 PO 8 PO 9 PO PO PO
10 11 12
CO 1 - - - 3 - - - - - - -

CO 2 - - 2 2 2 - - - - - 2 2

CO 3 - - 2 2 2 - - - - - 2 -

CO 4 - - 2 2 3 2 - - - - 2 2

Assessment Pattern
Bloom’s Category Continuous Assessment End Semester Examination
Tests
1 2
Remember 10 10 10
Understand 20 20 20
Apply 20 20 70
Analyse
Evaluate
Create
Mark distribution
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Total CIE ESE ESE Duration
Marks
150 50 100 3 hours

Continuous Internal Evaluation Pattern:

Attendance : 10 marks
Continuous Assessment Test (2 numbers) : 25 marks
Assignment/Quiz/Course project : 15 marks

End Semester Examination Pattern: There will be two parts; Part A and Part B. Part A
contain 10 questions with 2 questions from each module, having 3 marks for each question.
Students should answer all questions. Part B contains 2 questions from each module of
which student should answer any one. Each question can have maximum 2 sub-divisions
and carry 14 marks.

Course Level Assessment Questions

Course Outcome 1 (CO1): Differentiate various biological databases

1. How can you fetch the protein sequence data?

2. How can you retrieve the nucleotide sequence of haemoglobin?
3. How can you retrieve the 3D structure of a specific protein?

Course Outcome 2 (CO2): Infer the terminologies and concepts in the field

1. Define sequence alignment.

2. What do you infer when two protein sequences have 60% identity?
3. Differentiate between orthologs and paralogs.

Course Outcome 3(CO3):Generate and interpret the sequence alignment and implement
the scoring matrices

1. Differentiate Local and Global alignment.

2. Align two nucleotide sequences using Needleman Wunsch algorithm (match
score=+5, mismatch=-2, gap=-2)
3. Align two nucleotide sequences using Smith Waterman algorithm (match score=+5,
mismatch=-2, gap=-2)

Course Outcome 4 (CO4): Articulate the different bioinformatics tools

1. What is Pymol software used for?

2. Give example for multiple sequence alignment tools.
3. Explain the steps involved in homology modelling.
Model Question Paper

BIOTECHNOLOGY
Total Pages:
Reg No.:______________ Name:________________________
APJ ABDUL KALAM TECHNOLOGICAL UNIVERSITY
SIXTH SEMESTER B. TECH DEGREE EXAMINATION ________ ____ 20__
Course Code: BTT302
Course Name: BIOINFORMATICS
Max. Marks: 100 Duration: 3 Hours
PART A
Answer all questions, each carries 3 marks.
1 a) What is FASTA format? Give example.
b) Name any Chemical database. How it can be used?
c) Differentiate opening gap penalty and extension gap penalty.
d) What is blast used for?
e) Differentiate local and global sequence alignment

f) Differentiate PAM and BLOSUM matrices.

g) What is Genscan used for?

h) Name any 5 structure prediction software.

i) What is meant by docking?

j) Explain about any two tools used in CADD.

PART B
Answer any one full question from each module. Each carries 14 marks.

2 Point out the different bioinformatics tools and repositories that can be (14)
used to explore more about the biological data.

OR
3 How are biological databases classified? Explain in detail about each (14)
database.
4 Explain about the working of BLAST algorithm? Which are the different (14)
variants of BLAST?
OR
5 Briefly explain about the applications of Multiple Sequence Alignment. (14)
Illustrate with an example explain about the construction of a phylogenetic
tree using distance based method.
6 Align two nucleotide sequences using Needleman Wunsch algorithm (14)
(match score=+5, mismatch=-2, gap=-2)

OR
7 Align two nucleotide sequences using Smith Waterman algorithm (match (14)
score=+5, mismatch=-2, gap=-2)
8 BIOTECHNOLOGY
Explain the steps involved in homology modelling. Give example of (14)
homology modelling tools.
OR
9 Differentiate between the ab initio based and homology based gene (14)
prediction methods.
10 Summarise the steps involved in CADD. Give example of software used in (14)
the field.
OR
11 List out the names of any 2 visualization tools. Explain in detail about each. (14)
****

Syllabus

Module 1:

Introduction:Emergence of Bioinformatics, Applications in the field-Biological Databases-

Formats- Nucleic acid and Protein sequence Databases, Structure Databases, Chemical
Databases, Literature Databases

Module 2:

Biological Databases: Measurement of sequence similarity; Similarity and homology.

Pairwise sequence alignment: Basic concepts of sequence alignment, gap penalties,
Similarity search- BLAST, FASTA. Multiple Sequence Alignment, Phylogeny

Module 3:

Needleman and Wunsch, Smith and Waterman algorithms for pair-wise alignments,Use of
pair-wise alignments for analysis of Nucleic acid and protein sequences and interpretation
of results. PAM and BLOSUM

Module 4:

Gene prediction, Protein prediction, Structure prediction, Protein modeling, Internet

resources and basic principle underlying the in silico predictions.

Module 5:

3D structure visualization tools, Docking, Steps in Computational Aided Drug Discovery

(CADD), Tools and databases in CADD

Text Books

1. Teresa K Attwood, David J Parry-Smith, Introduction to bioinformatics, Pearson

Education. 1999
 2. Baxevanis A D, Francis Ouellellette B F, Bioinformatics- a Practical Guide to the
Analysis of Genes and Proteins, Wiley Interscience,2009.
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Reference Books

1. Jean-Michel Claverie, Cedric Notredame, Bioinformatics for Dummies, Wiley

Publishing Inc., 2007.

2. D W Mount, Bioinformatics: Sequence and Genome Analysis, 2/e, Cold Spring Harbor
Laboratory, Press, New York. 2004.

3. Jin Xiong, Essential Bioinformatics, Texas A& M University,Cambridge University Press,

2006.

Course Contents and Lecture Schedule

No Topic No. of Lectures

1 Introduction
1.1 Emergence of Bioinformatics, Applications in the field- 2
1.2 Nucleotide databases 1
1.3 Protein sequence databases 1
1.4 Structure databases 1
1.5 Chemical Databases 1

1.6 Literature Databases

1.7 Sequence formats Flat file, FASTA 1

1.8 Lab session
2.1 Sequence alignment, Terminologies; zones 1
2.2 Relevance of sequence comparison 1
2.3 BLAST Algorithm steps 1
2.4 Lab session 1
2.5 BLAST variants 1
2.6 FASTA working 1
2.7 Multiple sequence alignment applications 1
2.8 MSA methods 1
2.9 Phylogeny Terminologies 1
2.10 Methods of tree construction 2
3.1 Differentiate Local and Global Alignment 1
3.2 Smith Water man algorithm 2
3.3 Needleman Wunsch algorithm 2
3.4 PAM 2
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3.5 BLOSUM 1
3.6 Lab session 2
4.1 Gene prediction principles 2
4.2 Gene prediction resources 1
4.3 Structure prediction principle 1
4.4 Structure prediction resources 1
4.5 Lab session 2
4.6 Protein modelling 1
5.1 Tools in visualization 1
5.2 Lab 2
5.3 Basic concepts in docking 1
5.4 Steps in docking 1
5.5 CADD 2
5.6 Types of drug discovery –structure based and ligand based; 2
softwares; algorithms
5.7 Lab 2