B.sc. (Bioinformatics) Part III (Semester V & VI)

Outlines of Syllabi
for
B.Sc. (Bioinformatics) Part III (Semester V)
for
2013-14, 2014-15 and 2015-16 Sessions
Paper
Subject
Name of Paper
Introduction to Perl
Programming
II
III
IV
Fundamentals of Genomics
Molecular Modeling & Drug

Designing
Functional Genomics
Marks
No. of
Periods/week
Introduction to Perl
Programming
70
Practical
30
Fundamentals of Genomics
70
Practical
30
Molecular Modeling & Drug

Designing
70
Practical
30
Functional Genomics
70
Practical
30
SEMESTER V
PAPER I
INTRODUCTION TO PERL PROGRAMMING
Max. Marks: 70
Pass Marks: 35%
Lectures to be delivered: 75
(Each of 45 minutes duration)
Time Allowed: 3 Hours
INSTRUCTIONS FOR THE PAPER SETTER

The question paper will consist of three sections A, B and C. Section A and B will have
four questions from the respective section of syllabus and will carry 12 marks each. Section C
will consist of 11 short-answer type questions which will cover the entire syllabus uniformly and
will carry 22 marks in all.
INSTRUCTIONS FOR CANDIDATES
Candidates are required to attempt two questions from each section A and B and the
entire section C.
SECTION - A
1.
An Overview of Perl: File handles, operators, control structures regular expressions, list
processing; Variables, scalar values, context list, values and arrays, hashes; Typeglobs and
2.
file handles; Input Operators.

Urinary and binary operators, multiplicative operators, additive operators, shift operators,
3.
conditional operator.
Logical and, or, not, and or, C operators missing from Perl.
SECTION - B
4.
5.
Statements and declarations simple statements; If an unless statements; Loop statements.

Pattern Matching: Pattern matching operators, pragmatic modules, standard modules,
6.
subroutines.
Formats, format variables, data structures arrays, hashes.
Suggested Readings:
1. Programming Perl (2000) by L. Wall, T. Christiansen and J. Orwant, O'Reilly Media, USA.
2. Perl in a Nutshell (2002) by S. Spainhour, E. Siever and N. Patwardhan, O'Reilly Media,
USA.
3. Beginning Perl for Bioinformatics (2001) by J. Tisdall, O'Reilly Media, USA.
4. Mastering Perl for Bioinformatics (2003) by J. Tisdall, O'Reilly Media, USA.
PRACTICALS
2
Max Marks: 30
Pass Marks: 35%
List of Practicals
1. Writing code in PERL.
Practical Performance
Viva-Voce
Practical Record
: 22 Marks
: 5 Marks
: 3 Marks
PAPER II
FUNDAMENTALS OF GENOMICS
Max. Marks: 70
Pass Marks: 35%

entire section C.
SECTION - A
1.
History of genome sequencing project: The human genome project; The human genome
sequence, annotation (Repeats, coding regions, non-coding regions); Genome sizes;
2.
Genome sequencing strategies Hierarchical (clone contig) and Shotgun methods.

DNA sequencing methods: Manual and automated; Maxam-Gilbert and Sangers method,
3.
Chain termination method; DNA sequencing by capillary electrophoresis-only overview.

Base calling and sequence accuracy.
SECTION - B
4.
5.
6.
7.
Polymorphisms, repeats and single nucleotide polymorphisms (SNPs).

SNP detection methods: SSCP, PCR-based, dHPLC, sequencing.
SNP and disease; Molecular markers-RFLP, VNTR, RAPD, SSR, AFLP.
Managing and distributing genome data, web based servers and softwares for genome
analysis-ENSEMBL, VISTA, UCSC genome browser, NCBI genome.
Suggested Readings:
3
1. Introduction to Computational Molecular Biology (1997) by J.C. Setubal and J. Meidanis,

Brooks Cole Publishing Co., USA.
2. Bioinformatics: Sequence and Genome Analysis (2004) by D.W. Mount, Cold Spring Harbor
Laboratory Press, USA.
3. Genomics: The Science and Technology behind the Human Genome Project (2000) by C.
Cantor and C.L. Smith, Wiley-Inter Science, USA.
4. Genome Mapping - A Practical Approach (1997) by P.H. Dear, Oxford University Press, UK.
5. Principles of Genome Analysis and Genomes (2006) by S.B. Primrose and R.M. Twyman,
John Wiley and Sons, USA.
6. Post-Genomic Informatics (2001) by M. Kanehisa, Oxford University Press, USA.
PRACTICALS
Max Marks: 30
Pass Marks: 35%
List of Practicals
1. Human genome project
2. Sanger web page
3. SNP DETECTION
4. RFLP
5. ENSEMBL
6. VISTA
7. UCSC
Viva-Voce
Practical Record
: 22 Marks
: 5 Marks
: 3 Marks
PAPER III
MOLECULAR MODELING AND DRUG DESIGNING
Max. Marks: 70
Pass Marks: 35%
4

entire section C.
SECTION - A
1.
Useful concepts in molecular modeling: Coordinate systems, potential energy surfaces,
2.
molecular graphics, surfaces, computer hardware and software.

Force Fields: Bond stretching, angle bending, introduction to non-bonded interactions,
electrostatic interactions, Vander Waals interactions, hydrogen bonding in molecular
3.
mechanics.
Optimization of molecular geometrics: Empirical potential energy, molecular mechanics
force fields, energy minimization by systematic search method, mechanism approach,
molecular dynamics method.
SECTION - B
4.
Introduction to drug designing: Different approaches to drug designing, basic principles of

similarity and complementarity, high throughput versus rational drug designing, use of
5.
molecular visualization graphic packages e.g., RasMol, Cn3D, etc.

Basic concepts in quantitative structure activity relationship (QSAR): Objective of QSAR,
QSAR descriptors; Basic principles of docking a ligand in an active site of a target;
6.
Different methods of scoring and lead optimization - overview only.

The molecular modeling literature.
Suggested Readings:
1. Molecular Modeling Principles and Applications (2001) by A.R. Leach, Addison-Wesley
Longman Ltd., UK.
2. Molecular Dynamics Simulation Elementary Methods (1997) by J.M. Haile, John Wiley and
Sons, USA.
3. GROMOS 95 Manual (1995) BIOMOS, Switzerland.
4. HYPERCHEM Manual (1995) Hypercube, Canada.
5. Drug Design (2006) by V. Kothekar, Dhurb Publications, India.
PRACTICALS
5
Max Marks: 30
Pass Marks: 35%
List of Practicals
1. Molecular graphics packages: RasMol-viewing structures through Rasmol and other
softwares.
2. Protein explorer.
3. Docking/ligand binding softwares available on the web.
4. HEX SOFTWARE.
5. DRAGON SOFTWARE.
6. CN3D.
Viva-Voce
Practical Record
: 22 Marks
: 5 Marks
: 3 Marks
PAPER IV
FUNCTIONAL GENOMICS
Max. Marks: 70
Pass Marks: 35%

entire section C.
SECTION - A
1.
An introduction to microarray analysis, cDNA microarray technology, oligonucleotide
2.
microarray technology; Microarray databases; Applications of microarrays.

Microarray experimentation: Image processing; Normalizing expression measurements;
3.
4.
5.
Cluster analysis.
ESTs and EST databases, alternative splicing, differential display.
RNAi, snRNA, anti-sense RNA, micro RNA, SiRNA, regulatory RNA.
Secondary structure analysis of RNA: Stem and loop structure, RNA fold algorithm.
6
6.
Comparative genomics: Orthologues and paralogues, xenologues (horizontal gene transfer);

Non-orthologous gene displacement; Analogues; Orthologue identification by BLAST and
7.
reciprocal best hit.

Clusters of orthologous groups (COGs); Use of comparative genomics in gene annotation,
and function prediction; Phylogenetic foot printing; Synteny; Gene order.
SECTION - B
8.
9.
Use of comparative genomics in drug discovery programs.

Web based servers and softwares for genome analysis: Ensembl, NCSC genome browser,
10.
VISTA, NCBI genome.

Large genome alignments: Problems of complexity, repeats and size; MUMmer, BLASTZ,
11.
LAGAN, AVID, mVISTA, PIPMAKER.

Protein structure predictions; Fold recognition (threading); Protein folding - in vitro and in
12.
vivo (molecular chaperones), protein-ligand interactions.

Methods used for protein structure determination: X-ray and NMR structure determinations
13.
(Basic principles only).

Protein structure databases: SCOP, PDB.
Suggested Readings:
2. Discovering Genomics, Proteomics and Bioinformatics (2005) by A.M. Campbell and L.J.
Heyer, Benjamin Cummings, UK.
3. Proteins: Structures and Molecular Properties (1993) by T.E. Creighton, W.H. Freeman and
Company, USA.
4. Microarray Bioinformatics (2003) by D. Stekel, Cambridge University Press, UK.
PRACTICALS
Max Marks: 30
Pass Marks: 35%
List of Practicals
1. Using the STRINGS database: Phylogenetic profiling, gene fusions, operons
2. Using the COG database
3. Ensembl
4. Using the NCSC Genome browser
5. Using NCBI genome
6. Using the SCOP database.
7
Viva-Voce
Practical Record
: 22 Marks
: 5 Marks
: 3 Marks
Outlines of Syllabi
for
B.Sc. (Bioinformatics) Part III (Semester VI)
for
2013-14, 2014-15 and 2015-16 Sessions
Paper
V
Subject
Name of Paper
Database Systems
Database Systems
8
Marks
No. of
Periods/week
70
VI
VII
VIII
Introduction to Proteins and

Proteomics
Application of
Computational Biology
Biological Databanks and

Biodiversity
Practical
30
Introduction to Proteins and

Proteomics
70
Practical
30
Application of
Computational Biology
70
Practical
30
Biological Databanks and

Biodiversity
70
Practical
30
SEMESTER VI
PAPER V
DATABASE SYSTEMS
Max. Marks: 70
Pass Marks: 35%
9
entire section C.
SECTION - A
1.
Database system concepts and architecture: Data models, schemas, and instances, DBMS
2.
architecture and data independence.

Database modeling using ER model: Entity and entity sets, attributes, and keys;
3.
Relationships, relationship type, E-R models, E-R diagrams.

SQL: Data types, creating, tables, insertion, deletion, altering the contents of table,
renaming and destroying tables, data constraints; Basic queries in SQL, nested queries and
set comparisons, joins; Concept of views in SQL, granting and revoking permissions,
revoking privileges given.
SECTION - B
4.
Introduction to PL/SQL, processing a PL/SQL block, what is a cursor, error handling in
5.
PL/SQL; Stored procedures and functions; Database triggers.

Introduction to application development using visual basic; Working code and forms-basics
only; Various events and working with event handlers; Variables, procedures and functions;
Standard control, object browsing-basics only.
Suggested Readings:
1. Database System Concepts by H. Korth and A. Silberschatz, Tata Mc-Graw Hill Publications,
India.
2. An Introduction to Database Systems (2003) by C.J. Date, Addison-Wesley, USA.
3. Database System Organization (1977) by J.M. Martin, Prentice Hall, USA.
4. Oracle: Power Objects Handbook (1997) by B. Kolste, Tata McGraw Hill Education, USA.
PRACTICALS
Max Marks: 30
Pass Marks: 35%
List of Practicals
1. Writing codes with SQL.
10
Viva-Voce
Practical Record
: 22 Marks
: 5 Marks
: 3 Marks
PAPER VI
INTRODUCTION TO PROTEINS AND PROTEOMICS
Max. Marks: 70
Pass Marks: 35%

entire section C.
SECTION - A
1.
Proteins: Chemical properties of proteins, introduction to protein structures, physical

interactions that determine the property of proteins, short-range interactions, electrostatic
2.
forces, Van der Waals interactions, hydrogen bonds.

Proteins: Determination of sizes (Sedimentation analysis, gel filtration, SDS-PAGE);
3.
Native PAGE; Determination of protein structures - Edman degradation.

Post-translational modifications: Glycosylation, phosphorylation, lipid attachment,
disulphide bond formation.
SECTION - B
4.
Proteolytic processing: Protein localization and topology-membrane proteins; Secreted

proteins; ER/Golgi, Mitochondrial, chloroplast and nuclear localization of proteins; Non-
5.
ribosomal synthesis of unusual peptides.

Introduction to proteomics: The proteome, analysis of proteomes, 2D-PAGE, sample
preparation, solubilization, reduction, resolution, reproducibility of 2D-PAGE-overview
6.
only.
Mass spectrometry based methods for protein identification.
Suggested Readings:
11
1. Proteins: Structures and Molecular Properties (1993) by T.E. Creighton, W.H. Freeman and
Company, USA.
2. Proteomics: From Protein Sequence to Function (2002) by S.R. Pennington and M.J. Dunn,
Viva Books Private Limited, India.
3. Principles of Proteomics (2004) by R.M. Twyman, BIOS Scientific Publishers, UK.
Heyer, Benjamin Cummings, USA.
5. Introduction to Protein Science Architecture, Function and Genomics (2010) by A.M. Lesk,
Oxford University Press, USA.
6. Introduction to Proteomics - Tools for the New Biology (2001) by D.C. Liebler, Humana
Press, USA.
PRACTICALS
Max Marks: 30
Pass Marks: 35%
List of Practicals
1. SDS page.
2. 2 D MALDI-ToF design.
Viva-Voce
Practical Record
: 22 Marks
: 5 Marks
: 3 Marks
PAPER VII
APPLICATION OF COMPUTATIONAL BIOLOGY

Max. Marks: 70
Pass Marks: 35%

12

entire section C.
SECTION - A
1.
2.
Genome annotation: Computer tools for sequencing projects, comparative genomics tools.
Computational methods for gene identification: Signal based methods, content based
3.
4.
methods, homology based methods, performance measures; Prokaryotes versus eukaryotes.

Computational methods for gene prediction.
Statistical methods, compositional bias, machine-learning and probabilistic methods;
Artificial neural networks; Markov chain; Hidden Markov model.
SECTION - B
5.
Analysis of regulatory regions, signals and patterns, promoter prediction, transcription
6.
7.
8.
factor binding sites; Splice site recognition, repeat finders.

Analysis of membrane proteins; Hydropathy plots.
Sites: PSORT, PROSITE, PFAM.
Medical informatics: Introduction to clinical data management, hospital information
systems and electronic patient techniques, standards in health care and health care
informatics.
Suggested Readings:
1. Introduction to Computational Molecular Biology (1997) by J.C. Setubal and J. Meidanis,
Brooks Cole Publishing Co., USA.
3. Medical Informatics: Computer Applications in Healthcare and Biomedicine (2000) by G.
Wiederhold, E.L. Shortliff, L.M. Fagan and L.E. Perreault, Springer, USA.
Heyer, Benjamin Cummings, USA.
PRACTICALS
Max Marks: 30
Pass Marks: 35%
List of Practicals
1. Transcription factor databases like Transfac
2. Using PSORT
3. Using PROSITE
13
4. Using PFAM
5. Using hydropathy plots for analysis of membrane proteins
6. Using EXPASY
Viva-Voce
Practical Record
: 22 Marks
: 5 Marks
: 3 Marks
PAPER VIII
BIOLOGICAL DATABANKS AND BIODIVERSITY
Max. Marks: 70
Pass Marks: 35%

entire section C.
SECTION - A
1.
2.
3.
Biological diversity: Tree of life-Archaebacteria, eubacteria, eukaryota.

Species biodiversity: Taxonomic information on plants, animals, microbes, viruses.
Ecological diversity: Speciation and modes of speciation; Methods for species
4.
identification and classification; rRNA ribotyping.

Datasets in biodiversity informatics: Species 2000, Tree of life, ATCC, NBII, Species
5.
analyst collaboration, ICTV, Animal Viruses Information System, etc.

Applications of informatics in biodiversity.
SECTION - B
6.
7.
8.
Softwares for identification of species.

Delta, MicroIS; Need of metadata standards and ontology.
Introduction to VDLB: Data warehousing, data capture, data analysis; Managing the data;
9.
Data warehouse life cycle; Metadata and metadata catalogue; View maintenance, security.
Data mining models: Knowledge discovery in databases; Integration of data mining and
data warehousing; Data mining models; Statistic decision trees; Nearest neighbor and
clustering; Data visualization.
Suggested Readings:
14
1. Advances in Knowledge Discovery and Data Mining (1996) by U. Fayyad, G. PiatetskyShaprio, P. Smyth and R. Uthurusamy, MIT Press, UK.
2. Data Mining: Concepts and Techniques (2006) by J. Han and M. Kamber, Morgan
Kaufmann Publishers, USA.
3. The Data Warehouse Life Cycle Toolkit (2008) by R. Kimball, M. Ross, W. Thornthwaite, J.
Mundy and B. Becker, Wiley, USA.
4. Data Mining Techniques (2001) by A.K. Pujari, Universities Press, India.
5. Principles of Data Mining (2001) by D. Hand, H. Maniley and P. Smith, MIT Press, UK.
6. Biodiversity (2004) by C. Leveque and J.-C. Mounolou, Wiley, USA.
PRACTICALS
Max Marks: 30
Pass Marks: 35%
List of Practicals
1. Writing codes with SQL.
Viva-Voce
Practical Record
: 22 Marks
: 5 Marks
: 3 Marks
15

B.sc. (Bioinformatics) Part III (Semester V & VI)

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Outlines of Syllabi

Molecular Modeling & Drug

Molecular Modeling & Drug

INSTRUCTIONS FOR THE PAPER SETTER

file handles; Input Operators.

Statements and declarations simple statements; If an unless statements; Loop statements.

Pass Marks: 35%

INSTRUCTIONS FOR THE PAPER SETTER

Genome sequencing strategies Hierarchical (clone contig) and Shotgun methods.

Chain termination method; DNA sequencing by capillary electrophoresis-only overview.

Polymorphisms, repeats and single nucleotide polymorphisms (SNPs).

1. Introduction to Computational Molecular Biology (1997) by J.C. Setubal and J. Meidanis,

Pass Marks: 35%

INSTRUCTIONS FOR THE PAPER SETTER

Useful concepts in molecular modeling: Coordinate systems, potential energy surfaces,

molecular graphics, surfaces, computer hardware and software.

Introduction to drug designing: Different approaches to drug designing, basic principles of

molecular visualization graphic packages e.g., RasMol, Cn3D, etc.

Different methods of scoring and lead optimization - overview only.

Pass Marks: 35%

INSTRUCTIONS FOR THE PAPER SETTER

An introduction to microarray analysis, cDNA microarray technology, oligonucleotide

microarray technology; Microarray databases; Applications of microarrays.

Comparative genomics: Orthologues and paralogues, xenologues (horizontal gene transfer);

reciprocal best hit.

Use of comparative genomics in drug discovery programs.

VISTA, NCBI genome.

LAGAN, AVID, mVISTA, PIPMAKER.

vivo (molecular chaperones), protein-ligand interactions.

(Basic principles only).

Pass Marks: 35%

Introduction to Proteins and

Biological Databanks and

Introduction to Proteins and

Biological Databanks and

architecture and data independence.

Relationships, relationship type, E-R models, E-R diagrams.

Introduction to PL/SQL, processing a PL/SQL block, what is a cursor, error handling in

PL/SQL; Stored procedures and functions; Database triggers.

Pass Marks: 35%

INSTRUCTIONS FOR THE PAPER SETTER

Proteins: Chemical properties of proteins, introduction to protein structures, physical

forces, Van der Waals interactions, hydrogen bonds.

Native PAGE; Determination of protein structures - Edman degradation.

Proteolytic processing: Protein localization and topology-membrane proteins; Secreted

ribosomal synthesis of unusual peptides.

Pass Marks: 35%

APPLICATION OF COMPUTATIONAL BIOLOGY

INSTRUCTIONS FOR THE PAPER SETTER

INSTRUCTIONS FOR CANDIDATES

methods, homology based methods, performance measures; Prokaryotes versus eukaryotes.

Analysis of regulatory regions, signals and patterns, promoter prediction, transcription

factor binding sites; Splice site recognition, repeat finders.

Pass Marks: 35%

INSTRUCTIONS FOR THE PAPER SETTER

Biological diversity: Tree of life-Archaebacteria, eubacteria, eukaryota.

identification and classification; rRNA ribotyping.

analyst collaboration, ICTV, Animal Viruses Information System, etc.

Softwares for identification of species.

Pass Marks: 35%

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