School of Architecture, Science and technology
Yashwantrao Chavan Maharashtra Open University
Syllabus
V49: PG Diploma in
Bio-informatics
2011
AST, YCMOU, NASHIK – 422 222, MS, INDIA
CONTENTS
CONTENTS
Basic Information ................................................................................................................... 3
Programme Calendar.............................................................................................................. 3
Eligibility and Fees .................................................................................................................. 4
Semesters and Courses ........................................................................................................... 4
Evaluation Pattern.................................................................................................................. 5
Semester 01 ................................................................................................................................ 7
S11011: Basics of Bioinformatics............................................................................................. 7
Programme Information ........................................................................................................... 7
Course Information .................................................................................................................. 7
Presumed Knowledge and Learning Objectives ........................................................................ 7
Units ......................................................................................................................................... 7
Details Syllabus ......................................................................................................................... 8
Learning Resource Details ........................................................................................................ 9
S11012: Statistics for Bioinformatics ..................................................................................... 10
Programme Information ......................................................................................................... 10
Course Information ................................................................................................................ 10
Presumed Knowledge and Learning Objectives ...................................................................... 10
Units ....................................................................................................................................... 10
Details Syllabus ....................................................................................................................... 11
Learning Resource Details ...................................................................................................... 11
S11013: Basic Structural Biology ........................................................................................... 13
Programme Information ......................................................................................................... 13
Course Information ................................................................................................................ 13
Presumed Knowledge and Learning Objectives ...................................................................... 13
Units ....................................................................................................................................... 13
Details Syllabus ....................................................................................................................... 14
Learning Resource Details ...................................................................................................... 15
S11014: Object Oriented Programming and Web Publishing ................................................. 16
Programme Information ......................................................................................................... 16
Course Information ................................................................................................................ 16
Presumed Knowledge and Learning Objectives ...................................................................... 16
Units ....................................................................................................................................... 16
Details Syllabus ....................................................................................................................... 17
Learning Resource Details ...................................................................................................... 18
S11015: C++ Programming & Web Publishing Lab ................................................................. 19
Programme Information ......................................................................................................... 19
Course Information ................................................................................................................ 19
Presumed Knowledge and Learning Objectives ...................................................................... 19
Units ....................................................................................................................................... 19
Learning Resource Details ...................................................................................................... 20
Semester 02 ........................................................................................................................... 21
S11021: Database Management Systems .............................................................................. 21
Programme Information ......................................................................................................... 21
Course Information ................................................................................................................ 21
Presumed Knowledge and Learning Objectives ...................................................................... 21
Syllabus For V49: PG DIP (BIO-INF.)
Page 1
Units ....................................................................................................................................... 21
Details Syllabus ....................................................................................................................... 22
Learning Resource Details ...................................................................................................... 22
S11022: Biophysics ............................................................................................................... 24
Programme Information ......................................................................................................... 24
Course Information ................................................................................................................ 24
Presumed Knowledge and Learning Objectives ...................................................................... 24
Units ....................................................................................................................................... 24
Details Syllabus ....................................................................................................................... 25
Learning Resource Details ...................................................................................................... 25
S11023: Genomics and Proteomics ....................................................................................... 27
Programme Information ......................................................................................................... 27
Course Information ................................................................................................................ 27
Presumed Knowledge and Learning Objectives ...................................................................... 27
Units ....................................................................................................................................... 27
Details Syllabus ....................................................................................................................... 28
Learning Resource Details ...................................................................................................... 29
S11024: Computational Biology ............................................................................................ 30
Programme Information ......................................................................................................... 30
Course Information ................................................................................................................ 30
Presumed Knowledge and Learning Objectives ...................................................................... 30
Units ....................................................................................................................................... 30
Details Syllabus ....................................................................................................................... 31
Learning Resource Details ...................................................................................................... 31
S11025: Bioinformatics Lab................................................................................................... 33
Programme Information ......................................................................................................... 33
Course Information ................................................................................................................ 33
Presumed Knowledge and Learning Objectives ...................................................................... 33
Units ....................................................................................................................................... 33
Learning Resource Details ...................................................................................................... 34
Syllabus For V49: PG DIP (BIO-INF.)
Page 2
SYLLABUS FOR
V49: P G DIPLOMA COURSE IN BIOINFORMATICS
BASIC INFORMATION
1.
2.
3.
4.
5.
6.
Mode of Education: Full time residential face-to-face mode of education enhanced with
ELearning support.
Minimum Programme Duration: 3 years after HSC (12th) or Equivalent
Required Study Efforts: 720 Hours in each semester
Medium of Instruction: English
Attendance: Minimum 75% attendance for all courses.
Equivalence Status:
a.
UGC recognized and approved
b. DEC recognized and approved
c.
Recognized by Government of Maharashtra for MPSC jobs
PROGRAMME CALENDAR
SN Activity Description
Admission
01 Further Admission
02 Fresh Admission
Teaching - Learning
03 Teaching - Learning
04 Teaching–Learning Backlog Clearing
End Exam (EE) Form Submission
05 EE Form Submission by students at SC
06 EE Form Submission by SCs at University
Continuous Assessment (CA) Submission
07 CA Availability on website
08 CA Submission by Students at SC
09 Provisional CA Report by SCs
10 Final CA Report Submission by SCs at
University
End Examination (EE)
11 EE for Theory Courses
12 EE for Practical, STW, SV or PW Courses
Semester End Vacation
13 Semester End Vacation
Syllabus For V49: PG DIP (BIO-INF.)
Odd semesters like
01, 03, 05 and 07
From 01-Aug Till 31 Jan
Even semesters like
02, 04, 06 and 08
From 01-Feb Till 31-Jul
From 05-Jun Till 05-Jul
From 05-Jun Till 05-Aug
Not Offered
Not Offered
From 01-Aug Till 13 Nov From 01-Feb Till 16-May
From 14-Nov to 04-Dec From 17-May to 04-Jun
On or Before 30-Sep
On or Before 05-Oct
On or Before 31-Mar
On or Before 05-Apr
From 01-Aug Till 30 Nov From 01-Feb Till 30-May
01-30 Nov
01-30 May
On or before 31-Dec
On or before 30-Jun
On or before 31-Jan
On or before 31-Jul
From 05-Dec Till 14-Dec From 05-Jun Till 14-Jun
Immediately after the
Immediately after the
last day of end exam for last day of end exam for
theory courses, but
theory courses, but
positively before 05-Jan positively before 05-Jul
From 08-Jan Till 31-Jan
From 08-Jul Till 31-Jul
Page 3
ELIGIBILITY AND FEES
Admission Eligibility
Fresh B.Sc. or equivalent pass
Certification Eligibility
Fees and Deposit / Semester
Min 50% or as specified for the
Desc
INR
USD
respective course in the syllabus
UF
3,200
320
or better marks
SCF
12,000
1200
in total 10 courses (subjects)
ATF
of total 40 credit points
EF
130/T
13/T
at Semesters 01-02.
300/P
30/P
Aggregate performance and
Class in the programme shall be
reported on the basis of only
semesters 01-02.
Total ≈
LD
AFA
16,020
2,000
8040
1,602
200
804
SEMESTERS AND COURSES
SN
Code
Name
Semester 01: 16 CPs
01 S11011 Basics of Bioinformatics
02 S11012 Statistics for Bioinformatics
03 S11013 Basic Structural Biology
04 S11014 Object Oriented Programming and Web
Publishing
05 S11015 C++ Programming & Web Publishing Lab
Semester 02: 16 CPs
05 S11021 Data Base Management Systems
06 S11022 Bio-Physics
07 S11023 Genomics and Proteomics
08 S11024 Computational Biology
09 S11025 Bioinformatics Lab
Syllabus For V49: PG DIP (BIO-INF.)
CA
EE
TM Type CPs Passing
%
20
20
20
20
80
80
80
80
100
100
100
100
T
T
T
T
4
4
4
4
50%
50%
50%
50%
20
80
100
P
4
50%
20
20
20
20
20
80
80
80
80
80
100
100
100
100
100
T
T
T
T
P
4
4
4
4
4
50%
50%
50%
50%
50%
Page 4
EVALUATION PATTERN
SN
1
Type of
Course
Theory (T)
Continuous Assessment
1.
End Examination
Student is required to answer 1.
1 of 1 SAQ, each of 5 marks,
on each CP
2.
Single attempt only
Marks: 5 Marks for each CP
Duration: Specified 1 Month 3.
4.
5.
Student is required to submit 1.
“Activity Report” for each CP
in the prescribed format.
Single Attempt only
Marks: 5 Marks for each CP
Duration: Specified 1 Month
Student is required to answer 1 of
1 SAQ, each of 5 marks, on each CP
Student is required to answer 1 of
2.
2 LAQs, each of 15 marks, on each
3.
CP
4.
Maximum 5 Attempts only
Marks: 20 Marks for each CP
Duration: 45 minutes for each CP
2 Practical (P) 1.
External and internal examiners shall
assess each student based on:
a.
Conduct of One Randomly
2.
Selected Practical Activity – 5
3.
Marks
4.
b. Viva-Voice - 5 Marks
c.
Journal (Workbook) - 5 Marks
and
d. Report of Practical Activity - 5
Marks
2. Maximum 5 Attempts only
3. Marks: 20 Marks for each CP
4. Duration: 240 minutes
3 Project Work 5. Student is required to submit 5. External and internal examiners shall
(PW)
“Activity Report” for each CP
assess each student based on:
in the prescribed format.
a.
Project Proposal and Review of
6. Single Attempt only
Literature - 5 Marks
7. Marks: 5 Marks for each CP
b. Project Results and Report - 5
8. Duration: Specified 1 Month
Marks
c.
Presentation - 5 Marks and
d. Viva-Voce - 5 Marks
6. Maximum 5 Attempts only
7. Marks: 20 Marks for each CP
8. Duration: 90 minutes for each CP
The evaluation panel for practical and project type of course examination consists of internal as well as
external examiner (Appointed by university in consultation with Director of Regional center). Internal as well
as external examiner shall have 50% weightage in the assessment of each student. This evaluation panel
shall evaluate student’s performance as follows:
A. Evaluation Pattern for 4 C.P.Practical type of courses
SN
a
b
c
d
Description
Internal Examiner
Duration of End Exam: 240 minutes (4 hrs)
Actual Conduct of 1 randomly
8 Marks
selected practical activity
Viva-Voice
7 Marks
Workbook
8 Marks
Report of Practical Activity with
7 Marks
Diagram,
synoptic
Answers,
Syllabus For V49: PG DIP (BIO-INF.)
External Examiner
Total
Marks
Batch size: ≈15 students
13 Marks
21
12 Marks
13 Marks
19
21
19
12 Marks
Page 5
Graph/Observation and Conclusion
Total
30 Marks
50 marks
80 Marks
Actual CA and EE marks shall be used in computation of “Total Marks (TM)”. “Grace Factor” and
“Total Marks (TM)” shall be used in computation of Percentile marks. Only percentile marks shall
be reported for each course in the mark-statement. For successful completion, minimum 50%
marks shall be essential for each course. Only best of the past performance shall be reported.
Syllabus For V49: PG DIP (BIO-INF.)
Page 6
SEMESTER 01
S11011: BASICS OF BIOINFORMATICS
PROGRAMME INFORMATION
SN Description
1 University
2
3
4
5
School
Discipline
Level
Course Used in
Details
Yashwantrao Chavan Maharashtra Open University
Nashik - 422 222, Maharashtra, India
Website: http://www.ycmou.com/
School of Architecture, Science and Technology
Science
UG
V49:PG DIP (BIO-INF.)
COURSE INFORMATION
Sem Code Course Name
01 S11011 Basics of Bioinformatics
CP CST CAT ST CA EE TM Type
4 40 4 120 20 80 100 T
PRESUMED KNOWLEDGE AND LEARNING OBJECTIVES
Presumed Knowledge

Learning Objectives
After successful completion of this course,
student should be able to
Basic knowledge of Biology and

Make use of ICT in Bioinformatics and
computers

Understand various bioinformatics
resources
UNITS
UN Name of the Unit
1
Overview and Functions of a Computer System
CSs
CP Block 01
CSs
01-10
CP Block 02
2 Major Bioinformatics Resources
CSs
11-20
CP Block 03
3 Database Searches
4 Biodiversity Informatics
5 Applications of Bioinformatics in Various Fields
Syllabus For V49: PG DIP (BIO-INF.)
CSs
21-30
CP Block 04
CSs
Questions
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
Page 7
31-40
LAQs in end exam on
these units.
DETAILS SYLLABUS
UN Detail Syllabus of the Unit
CP
Block
Overview and functions of a Computer System:

Input and output devices.

Storage devices: Hard Disk, Diskette, Magnetic Tape, RAID, ZIP devices,Digital
Tape, CD-ROM, DVD, etc (capacity and access time).

Main Circuit Board of a PC: Chips, Ports, Expansion slots, etc. Memory:
CP
Register, buffer, RAM, ROM, PROM, EPROM, EEPROM (comparison).
1
Bock

Types of Processing: Batch, Real-Time, Online, Offline.
01

Types of modern computing: Workstations, Servers.

An overview of computer viruses: What is a virus? Virus symptoms, How do
they get transmitted? What are the dangers, General Precautions?

Introduction to operating systems: Operating System concept, Windows
2003/XP, Windows Vista, UNIX/LINUX.
Major Bioinformatics Resources:
Study of Major Bioinformatics Resources like NCBI, EBI, ExPASy, RCSB

The knowledge of various databases and bioinformatics tools available at
these resources, the major content of the databases, purpose and utility in
Life Science

Open access bibliographic resources and literature databases:

Open access bibliographic resources related to Life Sciences viz.,
CP
2

PubMed, BioMed Central, Public Library of Sciences (PloS).
Bock

keyword-based Entrz and SRS search ,
02

Sequence databases: Formats, querying & retrieval

Nucleic acid sequence databases: GenBank, EMBL, DDBJ

Protein sequence databases: SWISS-PROT, TrEMBL, PIR-PSD.

Proteomics– biochemical pathway databases – submitting sequence to the
databases
Database Searches:

Repositories for high throughput genomic sequences: EST, STS GSS, etc

Genome Databases at NCBI, EBI, TIGR, SANGER

Viral Genomes, Archeal and Bacterial Genomes

Eukaryotic genomes with special reference to model organisms (Yeast,
Drosophila, C. elegans, Rat, Mouse, Human, plants such as Arabidopsis
thaliana, Rice, etc.)·
CP
3

Structure Databases: PDB, NDB, PubChem· Derived Databases
Bock

Knowledge of the following databases with respect to: basic concept of
03
derived databases, sources of primary data and basic principles of the
method for deriving the secondary data, organization of data, contents and
formats of database entries, identification of patterns in given sequences and
interpretation of the same.

Sequence: Prosite, Pfamo Structure: CATH, SCOP, DSSP, PDB Goodies,
Extraction of knowledge from databases on Immunology, Plant, animal
Syllabus For V49: PG DIP (BIO-INF.)
Page 8
Biodiversity Informatics:

Definition, genetic diversity, species diversity, ecosystem diversity.
Biodiversity over geographic scales, _-diversity, _-diversity, _-diversity.
4
Distribution of biodiversity, hotspots of biodiversity, ecological and economic CP
role of biodiversity, scientific role and
Bock

Environmental economics. Threats to biodiversity.
04
Applications of Bioinformatics in Various Fields:
5

Environment, biotechnology, molecular biology, neurobiology, agriculture,
drug designing, biomedical genome medicines, medical microbiology.
LEARNING RESOURCE DETAILS
LR Code
Title
Author
Edition ISBN
Year Publisher
Text-Books
S11011-TB1
S11011-TB2
Reference-Books
S11011-RB1
Introduction to Bioinformatics
T. K. Attwood and D.J. Parry-Smith
2004
Introduction to Bioinformatics
2003
Arthur M. Lesk
Bioinformatics- Sequence, structure and databanks.
S11011-RB3
2000
D. Higgins and W. Taylor (Eds)
Bioinformatics: A practical Guide to the Analysis of
S11011-RB4 Genes and Proteins
1998
A. Baxevanis and B.F. Ouellette
S11011-RB2
S11011-RB5
Internet for the Molecular Biologist
S. R. Swindell, R.R.Miller and G.S.A.Myers (Eds.)
1996
The Internet for Cell and Molecular Biologists (2nd Edn.)
S11011-RB6 Andrea Cabibbo, Richard Grant and Manuela Helmer- 2004
Citterich (Eds.)
CD / DVD
S11011-CD1
S11011-CD2
Web Links
S11011-WL1
S11011-WL2
Syllabus For V49: PG DIP (BIO-INF.)
Pearson
Education
Ltd.,
New Delhi.
Oxford University
Press, New Delhi.
Oxford University
Press, New Delhi
Wiley-Interscience,
Hoboken, NJ.
Horizon Scientific
Press,
Wymondham, UK
Horizon scientific
Press,
Norwich,
UK.
Page 9
S11012: STATISTICS FOR BIOINFORMATICS
PROGRAMME INFORMATION
SN Description
1 University
2
3
4
5
School
Discipline
Level
Course Used in
Details
Yashwantrao Chavan Maharashtra Open University
Nashik - 422 222, Maharashtra, India
Website: http://www.ycmou.com/
School of Architecture, Science and Technology
Science
UG
V49:PG DIP (BIO-INF.)
COURSE INFORMATION
Sem Code Course Name
01 S11012 Statistics for Bioinformatics
CP CST CAT ST CA
4 40 4 120 20
EE
80
TM Type
100 T
PRESUMED KNOWLEDGE AND LEARNING OBJECTIVES
Presumed Knowledge

Knowledge of basic biology
Learning Objectives
After successful completion of this course,
student should be able to

Understand the statistical techniques
underlying various bioinformatics
algorithms
UNITS
UN Name of the Unit
CSs
CP Block 01
1 Basics of Statistics
CSs
01-10
CP Block 02
2 Probability Distribution
CSs
11-20
CP Block 03
3 Vectors and Regression Analysis
CSs
21-30
CP Block 04
4 Analysis and Hypothesis Testing
Syllabus For V49: PG DIP (BIO-INF.)
CSs
31-40
Questions
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Page 10
DETAILS SYLLABUS
CP
Block
UN Detail Syllabus of the Unit
Basics of Statistics

Functions and Graphs: Functions, Relations, notation and representation.
Graphs.

Review of basic functions. Functions of several variables.
CP
1
Bock

Basic trigonometric functions.
01

Matrix algebra: Addition, subtraction, multiplication, transpose, inverse.

Measures of central Tendency – Arithmetic Mean – Median – Mode –
Quartiles –Range – Quartile deviation – Mean deviation – Standard
Deviation.
Probability Distribution:

Probability – Addition Theorem – Multiplication Theorem - Baye’s Theorem
and related problems.
CP
2

Theoretical Distributions – Binomial, Poisson and Normal
Bock
02

Fitting of the Distributions and its properties - Z-score, P-value and E-value.

Sampling Distributors – Large and small sample tests – Student’s t0 test, X2
test, F-test – and Normal test and their applications.
Vectors and Regression Analysis:

Number integration. Interpolation and approximate methods. Concept of
Eigen vectors and eigen values. Poisson and extreme value distributions,
CP
3

Vector - addition, subtraction, dot, cross, scalar triple product, divergence Bock
03
and curl.

Methods of least squares, chi-square test, systematic and random sampling,
accidental and systematic errors, correlation and regression analysis.
Analysis and Hypothesis Testing

Multivariate analysis,

Hypothesis testing, Markov Models, HMM, Cluster analysis,
CP
4
Bock

Nearest neighbour search, Search using stem numbers,
04

Search using text signatures,

Phylogenetic analysis tools: Maximum Likelihood, Parsimony methods,
Analysis of Variance, f-test, t-test, and Graph theory in bioinformatics.
LEARNING RESOURCE DETAILS
LR Code
Title
Author
Edition
Year
ISBN
Publisher
Text-Books
Fundamentals of Mathematical Statistics, 2002
Sultan Chand & Sons, New
Delhi.
S11012-TB1 S.C. Gupta and V.K. Kapoor
11th
Edition.
S11012-TB2
Reference-Books
Statistical Methods
S11012-RB1
1996 Sultan Chand & Sons
S.P. Gupta
Syllabus For V49: PG DIP (BIO-INF.)
Page 11
S11012-RB2
Introduction to Biostatistics
L. Forthofer
S11012-RB3 Introduction to Biostatistics
Statistics Series).
Robert R. Sokal and F.J. Rohlf
CD / DVD
S11012-CD1
S11012-CD2
Web Links
S11012-WL1
S11012-WL2
Syllabus For V49: PG DIP (BIO-INF.)
1995
(Biology1987
Academic Press.
W.H. Freeman & Company,
New York.
Page 12
S11013: BASIC STRUCTURAL BIOLOGY
PROGRAMME INFORMATION
SN Description
1 University
2
3
4
5
School
Discipline
Level
Course Used in
Details
Yashwantrao Chavan Maharashtra Open University
Nashik - 422 222, Maharashtra, India
Website: http://www.ycmou.com/
School of Architecture, Science and Technology
Science
UG
V49:PG DIP (BIO-INF.)
COURSE INFORMATION
Sem Code Course Name
01 S11013 Basic Structural Biology
CP CST CAT ST CA
4 40 4 120 20
EE
80
TM Type
100 T
PRESUMED KNOWLEDGE AND LEARNING OBJECTIVES
Presumed Knowledge

Learning Objectives
After successful completion of this course,
student should be able to

Understand principles of structures of
Knowledge of nucleic acids and
macromolecules
proteins

Browse, visualise and analyse
structural data
UNITS
UN Name of the Unit
CSs
CP Block 01
1 Basics of Cell
CSs
01-10
CP Block 02
2 Principles of Protein
CSs
11-20
CP Block 03
3 Principles of Nucleic Acids Structures
CSs
21-30
CP Block 04
4 Structure-based Analyses
Syllabus For V49: PG DIP (BIO-INF.)
CSs
31-40
Questions
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Page 13
DETAILS SYLLABUS
UN Detail Syllabus of the Unit
CP
Block
Basics of Cell:

Cell as a basic unit of life, cell organization of prokaryotic and eukaryotic
CP
cells, structural and functional compartalization of cell; mitochondria,
1
Bock
chloroplast, lysosomes, cell wall, nucleus and nucleolus, protein translocation
01
in ER and vesicular transport into Golgi.

Cell cycle and its regulation; events during mitosis and meiosis.
Principles of Protein:

Classification of amino Acids. Classification and three-Dimensional structure
of proteins.

Overview of protein structure – Primary, Secondary, Tertiary and Quartenary
structures – J helix, K Pleated sheet,

Internal coordinates of proteins; Derivation and significance of CP
2
Ramachandran Map, protein folding and bonds stabilizing protein structure. Bock

Classification of enzymes, IUB system, enzyme substrate complex, active site 02
of enzymes, stereo specificity and ES complex formation,

Effect of temperature and pH and substrate concentration on reaction rate,
activation energy, transition state theory, enzyme activity.

Michaelis-Menten equation, significance of Vmax and Km, enzyme inhibition,
types of inhibitors and mode of action. Chemical modification of enzymes.
Principles of Nucleic Acids Structures:

purines and pyrimidines, nucleosides and nucleotides, DNA and RNA,
Watson-Crick model of DNA, A, B, & Z forms of DNA,

Tm and its relation to GC content, chemical and enzymatic degradation of
CP
nucleic acids. DNA binding proteins, RNA-Protein interactions. Various types
3
Bock
of interactions of DNA with proteins,
03

Small moleculer RNA, secondary and tertiary structures, t-RNA tertiary
structure.

Central dogma of protein synthesis: DNA Replication, transcription and
translation.
Structure-based Analyses:

Principles of Structural Organization and Conformational Analysis.

Basic Principles of X-ray Diffraction NMR, Mass Spectroscopy

Purpose of 3-D structure comparison and concepts,
CP

Visualization of structures using Rasmol or SPDBV or CHIME.
4
Bock

Basic concepts in molecular modeling: different types of computer
04
representations of molecules.

Concepts of force fields: representations of atoms and atomic interactions,
potential energy representation.

Algorithms such as FSSP, VAST and DALI, Fold Classes.
Syllabus For V49: PG DIP (BIO-INF.)
Page 14
LEARNING RESOURCE DETAILS
LR Code
Title
Author
Text-Books
S11013-TB1
S11013-TB2
Reference-Books
Principles of Physical Biochemistry
S11013-RB1
Van Holde
Basic one & two dimensional
S11013-RB2 sepectroscopy,
Horst Friebolin Witey
Edition
Year
ISBN
Publisher
Prentice Hall
NMR
1990
VCH
S11013-RB3
Lechninger Principles of Biochemistry –
David L. Nelson and Michael M. Cox.
3rd Edition
Macmillan worth Publishers.
S11013-RB4
Principles of Protein Structure,
G.E.Shuttz and R.H.Schirmer.
Springer –verlag, New York.
CD / DVD
S11013-CD1
S11013-CD2
Web Links
S11013-WL1
Syllabus For V49: PG DIP (BIO-INF.)
Page 15
S11014: OBJECT ORIENTED PROGRAMMING AND WEB
PUBLISHING
PROGRAMME INFORMATION
SN Description
1 University
2
3
4
5
School
Discipline
Level
Course Used in
Details
Yashwantrao Chavan Maharashtra Open University
Nashik - 422 222, Maharashtra, India
Website: http://www.ycmou.com/
School of Architecture, Science and Technology
Science
UG
V49:PG DIP (BIO-INF.)
COURSE INFORMATION
Sem Code Course Name
CP CST CAT ST CA
Object Oriented Programming and Web 4 40 4 120 20
01 S11014
Publishing
EE
80
TM Type
100 T
PRESUMED KNOWLEDGE AND LEARNING OBJECTIVES
Presumed Knowledge

Knowledge of C language and DBM
Learning Objectives
After successful completion of this course,
student should be able to

Understand organization of biological
data in databases and

Parse data for processing
UNITS
UN Name of the Unit
CSs
CP Block 01
1 Basics of C++
CSs
01-10
CP Block 02
Introduction to File, HTML, XML
2
CSs
11-20
CP Block 03
3 Scripting Languages Programming
CSs
21-30
CP Block 04
4
File handling and DBM using Perl
Syllabus For V49: PG DIP (BIO-INF.)
CSs
31-40
Questions
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
Page 16
these units.
DETAILS SYLLABUS
UN Detail Syllabus of the Unit
CP
Block
Basics of C++:

Introduction to the basic concepts of C++ language: Tokens, Keywords,
Identifiers, Data types, Variables, Manipulators – Expression and Control
structures.

Functions: Main function – function prototyping – call by reference – CP
1
function overloading – friend and inline functions.
Bock

Classes and objects – Constructors and Destructors – Operator overloading – 01
Type Conversions.

Inheritance – Single inheritance – Multiple inheritances – Hierarchical,
Hybrid inheritance – Polymorphism – Pointers – Console I/O operations.
Introduction to File, HTML, XML:

Files: classes for file stream operations, Opening, closing and processing file,
End of file detection File pointers

Error handling during file operations: Command line arguments, Exception
handling.
CP
2

The Internet and its Resources: World Wide Web (WWW): Associated tools,
Bock
services, resources and various terminologies. Browser – Designing web site
02
– Basics of creating a web page

HTML – Basics, Tags, Text handling, Image handling, Links, Frames and
Tables.

XML – Basics, data binding and record sets.
Scripting Languages Programming:
Introduction: What is Perl? Why use Perl in Bioinformatics? History of Perl, Availability,
Support,

Basic Concepts.
o
Scalar Data: What is Scalar Data?, Numbers, Strings, Scalar
Operators, Scalar Variables, Scalar Operators and Functions.
o
Arrays and List Data: What is a List or Array? Literal
Representation, Variables, Array Operators and Functions, Scalar
and List Context.
CP
3
o
Hashes: What is a Hash? Hash Variables, Literal Representation of Bock
a Hash, Hash Functions, Hash Slices.
03
o
Basic I/O.

Control Structures: Statement Blocks. Miscellaneous Control Structures.

Regular Expressions: Concepts About Regular Expressions, Simple Uses of
Regular Expressions, Patterns, More on the Matching Operator,
Substitutions, The split and join Functions

Subroutines: System and User Functions, The local Operator, Variable-length
Parameter Lists, Notes on Lexical Variables.
File handling and DBM using Perl:
CP

Filehandles and File Tests: What Is a Filehandle? Opening and Closing a
4
Bock
Filehandle, Using Pathnames and Filenames, A Slight Diversion: die, Using
04
Filehandles, The -xFile Tests, The stat Function Formats: What Is a Format?
Syllabus For V49: PG DIP (BIO-INF.)
Page 17








Defining a Format, Invoking a Format.
Directory Access: Moving Around the Directory Tree, Globbing, Directory
Handles, Opening and Closing a Directory Handle, Reading a Directory
Handle.
File and Directory Manipulation
Process Management: Using system and exec, Using Backquotes.
Other Data Transformation: Finding a Substring, Extracting and Replacing a
Substring. Formatting Data: Sorting, Transliteration.
Database Manipulation: DBM Databases and DBM Hashes, Opening and
Closing DBM Hashes, Fixed-Length Random-Access Databases, VariableLength (Text) Databases, and Win32 Database Interfaces.
CGI Programming: The CGI.pm Module, Your CGI Program in Context,
Simplest CGI Program, Passing Parameters via CGI, Perl and the Web.
Object oriented perl: Introduction to modules, Creating Objects.
Bioperl: Introduction, Installation procedures, Architecture, Uses of bioperl.
LEARNING RESOURCE DETAILS
LR Code
Title
Author
Edition ISBN
Year Publisher
Text-Books
Object Oriented Programming with C++
E Balagurusamy
Web Publishing
S11014-TB2
Monica D’Souza & Jude D’Souza.
Reference-Books
Object Oriented Programming in C++
S11014-RB1
Robert Lafore, Galgotia
Let us C++
S11014-RB2
Yeshwant Kanetkar
TMH.
S11014-TB1
S11014-RB3
Instant HTML Programmer’s Reference
Steve Wright
2001
BPB
WROX Press Ltd.
CD / DVD
S11014-CD1
S11014-CD2
Web Links
S11014-WL1
S11014-WL2
Syllabus For V49: PG DIP (BIO-INF.)
Page 18
S11015: C++ PROGRAMMING & WEB PUBLISHING LAB
PROGRAMME INFORMATION
SN Description
1 University
2
3
4
5
School
Discipline
Level
Course Used in
Details
Yashwantrao Chavan Maharashtra Open University
Nashik - 422 222, Maharashtra, India
Website: http://www.ycmou.com/
School of Architecture, Science and Technology
Science
UG
V49:PG DIP (BIO-INF.)
COURSE INFORMATION
Sem Code Course Name
01 S11015 C++ Programming & Web Publishing Lab
CP CST CAT ST CA
4 60 4 120 20
EE
80
TM Type
100 P
PRESUMED KNOWLEDGE AND LEARNING OBJECTIVES
Presumed Knowledge

Knowledge of S11014
Learning Objectives
After successful completion of this course,
student should be able to

Perform practical related to C, C++
and Web publishing language.
UNITS
Note: A journal of practical work performed during the year is required to be maintained. A
minimum of 20 experiments are expected to be performed
CP
UN Details of the Activities
Questions
Block
1-1 Write a Perl program to Convert DNA sequence into RNA sequence.
Students
Write a Perl program to get anti-parallel and complementary strand of a
1-2
CP
have to
given DNA strand.
Bock
submit
1-3 Write a Perl program to join two different sequences of a given DNA.
01 ‘Report of
1-4 Write a Perl program to open NCBI database file by File-handle.
Activities’
1-5 Write a Perl program to search motif.
CSs in CA and
1-6 Write a Perl program to count the bases present in DNA molecule
01-25 face Viva
Calculations of Mean, median, mode and standard deviation using C
for end
1-7
programming language.
exam on
1-8 Write a C Program to print a series of odd/even numbers
these
1-9 Program to find whether a given number is prime or not
units.
1-10 Program to check whether a string is palindrome or not
Creating a web page to get protein sequence data and compute and
1-11
display amino acid composition
Creating a web page to get nucleic acid sequence data and compute and
1-12
display base composition
1-13 Web site navigation to enzyme database
1-14 To visualize the structure of DNA (A-, B- & Z- form), DNA-binding Proteins
Syllabus For V49: PG DIP (BIO-INF.)
Page 19
1-15
1-16
1-17
1-18
1-19
1-20
1-21
1-22
1-23
1-24
1-25
Browsing Human genome data, OMIM, SNP databases to understand
Genetic and metabolic disorders
To Display Secondary Structure of RNA Molecules
Browsing genomic resources for plant, yeast genomes
Browsing resources for microbial and viral genome.
Literature mining using pubmed, pubmed central and Medline
Retrieving Protein and DNA Sequences using Entrez at NCBI
Retrieving Protein and DNA Sequences using SRS at EBI
Website navigation to PDB, swissprot, uniprot and ccsd.
Explore: Derived databases of structures: DSSP, FSSP, CATH & SCOP
To study different visualization tools.
To Perform FASTA Search for DNA And Protein Data.
LEARNING RESOURCE DETAILS
LR Code
Title
Author
Edition ISBN
Year Publisher
Text-Books
S11015-TB1
S11015-TB2
Reference-Books
S11015-RB1
CD / DVD
S1101-CD1
S11015-CD2
Web Links
S11015-WL1
S11015-WL2
Syllabus For V49: PG DIP (BIO-INF.)
Page 20
SEMESTER 02
S11021: DATABASE MANAGEMENT SYSTEMS
PROGRAMME INFORMATION
SN Description
1 University
2
3
4
5
School
Discipline
Level
Course Used in
Details
Yashwantrao Chavan Maharashtra Open University
Nashik - 422 222, Maharashtra, India
Website: http://www.ycmou.com/
School of Architecture, Science and Technology
Science
UG
V49:PG DIP (BIO-INF.)
COURSE INFORMATION
Sem Code Course Name
01 S11021 Database Management Systems
CP CST CAT ST CA
4 40 4 120 20
EE
80
TM Type
100 T
PRESUMED KNOWLEDGE AND LEARNING OBJECTIVES
Presumed Knowledge

Basic knowledge about databases
Learning Objectives
After successful completion of this course,
student should be able to

Handle various databases effectively
and apply it properly

Understand basics of SQL, JAVA
UNITS
UN Name of the Unit
CSs
CP Block 01
1 Database Concept and Data Models
CSs
01-10
CP Block 02
2 SQL and its Application
CSs
11-20
CP Block 03
3 Introduction to JAVA Programming
CSs
21-30
CP Block 04
4 Interactive Graphics and JAVA Applications
Syllabus For V49: PG DIP (BIO-INF.)
CSs
31-40
Questions
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
Page 21
these units.
DETAILS SYLLABUS
CP
Block
UN Detail Syllabus of the Unit
Database Concept and Data Models:

Introduction to Database Systems: Concepts of various types of databases,
Data Abstraction., Instances & Schemes.

E-R Model: Entity and entity sets, Relations and relationship sets, E-R CP
1
diagrams, Reducing E-R Diagrams to tables.
Bock

Data Models: Network Data Model: Basic concepts, Hierarchical Data Model: 01
Basic Concepts. Multimedia Databases - Basic Concepts and Applications,
Indexing and Hashing. Text Databases.
SQL and its Application:

SQL: Select Statements, Data Definition Statements, Data Manipulation
Statements, Data Control Statements, Other Database Objects, View,
Sequences, Synonyms

Front End Development: Introduction to Application Development using
CP
2
Visual Basic, Working with Code and Forms, Variables, Procedures and
Bock
Controlling Program Executor, Standard Controls, Data Access Using Data
02
Control,

Connecting to Oracle Database using Visual Basic: Acquiring the skills of
using Oracle DBMS as backend, SQL skills and basic skill infusing VB as a front
end.
Introduction to JAVA Programming:

Introduction to JAVA Programming: Object-oriented programming and
JAVA;

JAVA Basics— Working with Objects, Strings, variant, Constant, Arrays,
3
Conditionals and Loops, Iterative Statements, Declarations and Access CP
Bock
Controls.

Classes and Objects in JAVA: Creating Classes in JAVA and Applications e.g., 03
Applets basics, Inbuilt classes & Application, Layout Mg, Graphics, Fonts &
Colour, Images & Sound.
Interactive Graphics and JAVA Applications:

Simple Animation & Treads, Advanced animation,

AWT Components,

Advanced GUI Components,
4

Event Handling, Swings, Multitreading,

Working with Data Structures

BioJAVA
CP
Bock
04
LEARNING RESOURCE DETAILS
LR Code
Title
Author
Text-Books
S11021-TB1 Computer Database Organisation
Syllabus For V49: PG DIP (BIO-INF.)
Edition
Year
ISBN
Publisher
Prentice Hall of India
Page 22
James Martin
S11021-TB2
Reference-Books
Principles of Database Management
S11021-RB1
James Martin
An Introduction to Database systems
S11021-RB2
C.J. Date
Database Management System
S11021-RB3
Bipin Desai
CD / DVD
S11021-CD1
S11021-CD2
Web Links
S11021-WL1
S11021-WL2
Syllabus For V49: PG DIP (BIO-INF.)
Prentice Hall of India
3rd
Narosa Publishing House
Page 23
S11022: BIOPHYSICS
PROGRAMME INFORMATION
SN Description
1 University
2
3
4
5
School
Discipline
Level
Course Used in
Details
Yashwantrao Chavan Maharashtra Open University
Nashik - 422 222, Maharashtra, India
Website: http://www.ycmou.com/
School of Architecture, Science and Technology
Science
UG
V49:PG DIP (BIO-INF.)
COURSE INFORMATION
Sem Code Course Name
01 S11022 Biophysics
CP CST CAT ST CA EE TM Type
4 40 4 120 20 80 100 T
PRESUMED KNOWLEDGE AND LEARNING OBJECTIVES
Presumed Knowledge

Learning Objectives
After successful completion of this course,
Basic knowledge of Biophysical student should be able to
techniques and Physics in H.S.S.C.
 Explain the Biophysical Techniques
UNITS
UN Name of the Unit
CSs
CP Block 01
1 Basics of Physics and Chemical Kinetics
CSs
01-10
CP Block 02
2 Introduction to Biophysical Techniques
CSs
11-20
CP Block 03
3 Chromatography and Mass Spectroscopy
CSs
21-30
CP Block 04
4 Simulation Techniques and Drug Discovery
Syllabus For V49: PG DIP (BIO-INF.)
CSs
31-40
Questions
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Page 24
DETAILS SYLLABUS
CP
Block
UN Detail Syllabus of the Unit
Basics of Physics and Chemical Kinetics:

Methods for determining free energy changes, coupled reaction, kinetics of
reaction, activation energy.

Polar molecules, molar refraction and polarization. Dipole moment,
CP
1
potentiometric determination of pK of amino acids.
Bock

Free energy of charged metal ions; Hydration and solvation number. Non01
covalent bonding in protein structure.

Basic principle of chemical kinetics – Zero order and first order kinetics,
energy of activation, Derivative and differential
Introduction to Biophysical Techniques:

Biophysical Techniques for determining size and shape of macromolecules –
ultra centrifugation, electrophoresis and chromatography.
CP
2

Application of spectroscopy (fluorescence and absorption spectroscopy)
Bock

X-ray diffraction for determination of biomolecular secondary and tertiary
02
structure – CD, NMR, X-ray crystallography, mass spectroscopy of biological
molecules.
Chromatography and Mass spectroscopy:

2-D gel electrophoresis, gel filtration, PAGE, isoelectrick focusing, affinity
chromatography, HPLC, ICAT, fixing and spot visualization,

Mass spectroscopy for protein analysis, MALDI-TOF, Electrospray ionization CP
3
(EST), Tandem mass spectroscopy (MS/MS) analysis; tryptic digestion and Bock
peptide fingerprinting (PMF),
03

Protein Micro array in protein expression, profiling and diagnostics, drug
target discovery.
Simulation Techniques and Drug Discovery:

Geometry optimization algorithms: Steepest descent, conjugate
gradient.

Various Simulation Techniques: MD, Monte Carlo, docking
strategies etc.
CP

Molecular mechanics, conformational searches.
4
Bock

Drug discovery process.
04

Role of Bioinformatics in drug design.

Target identification and validation, lead optimization and
validation.

Structure-based drug design and ligand based drug design.

Modeling of target-small molecule interactions.
LEARNING RESOURCE DETAILS
LR Code
Title
Author
Edition
Year
ISBN
Publisher
Text-Books
S11022-TB1
Syllabus For V49: PG DIP (BIO-INF.)
Page 25
S11022-TB2
Reference-Books
Biophysical Chemistry Part – I, II & III
S11022-RB1 C.R. Cantor & P.R. Schimmel
Introduction to Protein Structure
C. Branden and J. Tooze
Biophysics
S11022-RB3
R. Glaser
CD / DVD
S11022-CD1
S11022-CD2
Web Links
S11022-WL1
S11022-WL2
S11022-RB2
Syllabus For V49: PG DIP (BIO-INF.)
1980
1991
2000
W.H. Freeman & Co., in San
Fransisco
Garland
Publishing Inc. New York.
Springer
Page 26
S11023: GENOMICS AND PROTEOMICS
PROGRAMME INFORMATION
SN Description
1 University
2
3
4
5
School
Discipline
Level
Course Used in
Details
Yashwantrao Chavan Maharashtra Open University
Nashik - 422 222, Maharashtra, India
Website: http://www.ycmou.com/
School of Architecture, Science and Technology
Science
UG
V49:PG DIP (BIO-INF.)
COURSE INFORMATION
Sem Code Course Name
01 S11023 Genomics and Proteomics
CP CST CAT ST CA
4 40 4 120 20
EE
80
TM Type
100 T
PRESUMED KNOWLEDGE AND LEARNING OBJECTIVES
Presumed Knowledge
Learning Objectives
After successful completion of this course,
Course Prerequisites:

Basic knowledge of genetics, heredity student should be able to
and gene

Comprehend
the
essential
information in understanding the
basis of heredity that is useful in
having clarity about the background

Give an essential basis of the
prokaryotic and eukaryotic genome as
such and the genes and sequencing
etc.
UNITS
UN Name of the Unit
CSs
CP Block 01
1 Basics of Genetics
CSs
01-10
CP Block 02
2
r-DNA technology and Genomics
CSs
11-20
CP Block 03
3 Gene Expression and DNA Microarray
4
CSs
21-30
CP Block 04
Secondary Structure Prediction
Syllabus For V49: PG DIP (BIO-INF.)
Questions
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
Page 27
CSs
31-40
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
DETAILS SYLLABUS
UN Detail Syllabus of the Unit
Basics of Genetics:

Mendelian principles of inheritance, sex linked inheritance.

Concept of linkage, linkage maps and recombination.

Mutations – molecular, gene/point and chromosomal types.

Phenotype and genotype relationships, role of environment, from gene to
1
phenotype, gene interactions. Study of quantitative traits.

Genetics of populations, genetics and evolution. X-linked and autosomal
diseases, mitochondrial related disease, QTL methods for diagnostics.

Extra chromosomal inheritance.

Molecular genetics and genetic disorders.
CP
Block
CP
Bock
01
r-DNA technology and Genomics:

Cloning vectors, concept of maps, physical maps, shotgun libraries, DNA
polymorphism, nucleotides and DNA sequences.

Recombinant DNA technology, restriction enzymes, resource for restriction
enzyme (REBASE),

Polymerase chain reaction, primer selection for PCR, BLASTn, application of
CP
2
BioEdit.
Bock

Genome information and special features, coding sequences (CDS),
02
untranslated regions (UTR’s), cDNA library, expressed sequence tags (EST).

Approach to gene identification; masking repetitive DNA, database search,
codon-bias detection, detecting functional sites in the DNA.

Internet resources for gene identification, detection of functional sites, gene
expression.
Gene Expression and DNA Microarray:

Introduction, Basic steps for gene expression, concept of microarrays;
spotted arrays, oligonucleotide arrays,

designing the experiment, Two-color microarray experiments, Clustering
gene expression profiles; Agglomerative, Hierarchical, Nearest neighbour CP
3
(Single-linkage), complete-linkage, average-linkage, weighed pair-group Bock
average, k-means clustering, self-organizing maps (SOM) clustering,
03

Tools for microarray analysis; soft-finder, xCluster, MADAM, SAGE,
Microarray design, microarray experimentation, fabrication computational
analysis of Microarray data, Applications of microarray technology.
Secondary Structure Prediction:

Algorithms of Chou Fasman, GOR methods;canalysis of results and measuring
the accuracy of predictions using Q3, Segment
overlap, Mathew’s CP
4
correlation coefficient.
Bock
Tertiary Structure prediction:
04

Fundamentals of the methods for 3D structure prediction (sequence
similarity / identity of target proteins of known structure,fundamental
Syllabus For V49: PG DIP (BIO-INF.)
Page 28


principles of protein folding etc.)
Homology Modeling; fold recognition, threading approaches, and ab-initio
structure prediction methods.
Fundamentals of docking small and macromolecules to proteins and nucleic
acids.
LEARNING RESOURCE DETAILS
LR Code
Title
Author
Edition
Year
ISBN
Publisher
Text-Books
S11023-TB1
S11023-TB2
Reference-Books
S11023-RB1
S11023-RB2
CD / DVD
S11023-CD1
S11023-CD2
Web Links
S11023-WL1
S11023-WL2
Syllabus For V49: PG DIP (BIO-INF.)
Page 29
S11024: COMPUTATIONAL BIOLOGY
PROGRAMME INFORMATION
SN Description
1 University
2
3
4
5
School
Discipline
Level
Course Used in
Details
Yashwantrao Chavan Maharashtra Open University
Nashik - 422 222, Maharashtra, India
Website: http://www.ycmou.com/
School of Architecture, Science and Technology
Science
UG
V49:PG DIP (BIO-INF.)
COURSE INFORMATION
Sem Code Course Name
01 S11024 Computational Biology
CP CST CAT ST CA
4 40 4 120 20
EE
80
TM Type
100 T
PRESUMED KNOWLEDGE AND LEARNING OBJECTIVES
Presumed Knowledge

Learning Objectives
After successful completion of this course,
student should be able to
Basic knowledge of biology and bio
Analyse molecular sequence data
informatics and primary databases
using various sequence-based
bioinformatics approaches
UNITS
UN Name of the Unit
CSs
CP Block 01
1 Scoring Matrices and Sequence Analysis
CSs
01-10
CP Block 02
2
Pairwise Sequence Alignments
3
Multiple Sequence Alignments (MSA)
CSs
11-20
CP Block 03
4 Sequence Patterns and Profiles
5 Taxonomy and Phylogeny
CSs
21-30
CP Block 04
6 Phylogenetic Analysis and Algorithms
Syllabus For V49: PG DIP (BIO-INF.)
CSs
31-40
Questions
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Students have to answer
'1 of 1' SAQ in CA and
'1 of 1' SAQ & '1 of 2'
LAQs in end exam on
these units.
Page 30
DETAILS SYLLABUS
CP
Block
UN Detail Syllabus of the Unit
Scoring Matrices and Sequence analysis:

Basic concepts of sequence similarity, identity and homology, definitions of
homologues, orthologues, paralogues.

Scoring matrices: basic concept of a scoring matrix, Matrices for nucleic acid
CP
1
and proteins sequences, PAM and BLOSUM series, principles based on which
Bock
these matrices are derived.
01

Sequence-based: BLAST & FASTA, Use of these methods for sequence
analysis including the on-line use of the tools and interpretation of results
from various sequence and structural as well as bibliographic databases.
Pairwise sequence alignments:

Basic concepts of sequence alignment, Needleman & Wunsch, Smith &
2
Waterman algorithms for pairwise alignments, use of pairwise alignments for
analysis of Nucleic acid and protein sequences and interpretation of results.
CP
Multiple sequence alignments (MSA):
Bock

The need for MSA, basic concepts of various approaches for MSA (e.g.
02
3
progressive, hierarchical etc.). Algorithm of CLUSTALW and PileUp and their
application for sequence analysis (including interpretation of results),
concept of dendrogram and its interpretation.
Sequence Patterns And Profiles:

Basic concept and definition of sequence patterns, motifs and profiles,
4
various types of pattern representations viz. consensus, regular expression
(prosite-type) and profiles; profile-based database searches using PSI-BLAST,
CP
analysis and interpretation of profile-based searches.
Bock
Taxonomy and Phylogeny:

Basic concepts in systematics, taxonomy and phylogeny; molecular evolution; 03
5
nature of data used in Taxonomy and Phylogeny, Definition and description
of phylogenetic trees and various types of trees.
Phylogenetic Analysis and Algorithms:

Phylogenetic analysis algorithms such as Maximum Parsimony, UPGMA,
Transformed Distance, Neighbors-Relation, Neighbor-Joining;
CP
6

Probabilistic models and associated algorithms such as Probabilistic models Bock
of evolution and Maximum likelihood algorithm,
04

Bootstrapping method,

Use of tools such as Phylip, Mega, PAUP.
LEARNING RESOURCE DETAILS
LR Code
Title
Author
Text-Books
S11024-TB1
S11024-TB2
Reference-Books
S11024-RB1 Bioinformatics: A practical guide to the
Syllabus For V49: PG DIP (BIO-INF.)
Edition
Year
2001
ISBN
Publisher
Willey Interscience
Page 31
analysis of genes and proteins.
AD Baxevanis & BFF Ouellette
Bioinformatics: Methods and Protocols –
S11024-RB2 Stephen Misener & Stephen A. Krawetz
S11024-RB3
Bioinformatics: Sequence, structure and
databanks – Des Higgins & Willie Taylor.
New York.
2000
Humana Press
New Jersey
2000
Oxford University Press
CD / DVD
S11024-CD1
S11024-CD2
Web Links
S11024-WL1
S11024-WL2
Syllabus For V49: PG DIP (BIO-INF.)
Page 32
S11025: BIOINFORMATICS LAB
PROGRAMME INFORMATION
SN Description
1 University
2
3
4
5
School
Discipline
Level
Course Used in
Details
Yashwantrao Chavan Maharashtra Open University
Nashik - 422 222, Maharashtra, India
Website: http://www.ycmou.com/
School of Architecture, Science and Technology
Science
UG
V49:PG DIP (BIO-INF.)
COURSE INFORMATION
Sem Code Course Name
01 S11025 Bioinformatics Lab
CP CST CAT ST CA
4 60 4 120 20
EE
80
TM Type
100 P
PRESUMED KNOWLEDGE AND LEARNING OBJECTIVES
Presumed Knowledge
Learning Objectives
After successful completion of this course,
Course Prerequisites:

Knowledge of Computational Biology, student should be able to
Genomics
and
Bioinformatics

Perform practical related to BioApproaches
Informatics, Graphics and Genomics
UNITS
Note: A journal of practical work performed during the year is required to be maintained. A
minimum of 20 experiments are expected to be performed
CP
UN Details of the Activities
Questions
Block
1-1 To write a query to show Use of operators.
Students
1-2 To write a query to show Checking null condition
CP
have to
1-3 To write a query to show Union operators.
Bock
submit
1-4 To write a query to show Union ALL operators.
01 ‘Report of
1-5 To write a query to find query by using ‘in’ clause.
Activities’
CSs in CA and
1-6 To write a query to find query by using ‘‘exist’ clause.
To write a query to show that arithmetic expression can be used in select 01-25 face Viva
1-7
for end
clause and rename unnamed attributes.
exam on
1-8 To Creating Tables in the Oracle Database.
these
1-9 To Perform Data Manipulation operations.
units.
1-10 Write a Java program to displaying general form of a class.
1-11 Write a Java program to create child fram window from within an applet.
Write a Java program to create an applet that sets the forgroundand
1-12
background colors and outputs a string.
Mining genomic data to identify genomic features: codon usage, repeats,
1-13 reversals, Homologous regions, operon structures, syntenic regions,
horizontal gene transfer
1-14 Gene prediction algorithms for Prokaryotes
1-15 Gene prediction algorithms for Eukaryotes
Syllabus For V49: PG DIP (BIO-INF.)
Page 33
1-16
1-17
1-18
1-19
1-20
1-21
1-22
1-23
1-24
1-25
To perform Global Alignment Of Two Different Sequence Using Needle
and Wünsch Algorithm.
To Perform Local Alignment Of Two Different Sequence Using Smith
Waterman Algorithm.
To Perform Sequence Alignment of Two Different Sequence Using
Various Scoring Matrices and Combination of Penalty Value To Use And
Understand BLAST Series: BLASTN, BLASTP, BLASTX, TBLASTN
To Use and Understand BLAST Series: PHI-BLAST, PSI-BLAST
To Perform Multiple Sequence Alignment Using Clustal W Series.
To Study The Phylip Phylogenetic Package .
To Study Molecular Phylogeny Using Distance Methods / Phenetic
Approach.
To Study Molecular Phylogeny Using Parsimony Method / Characterbased Methods
Prediction of secondary structures of proteins
Prediction of Tertiary structure fo proteins: SwissModel and Modeller
LEARNING RESOURCE DETAILS
LR Code
Title
Author
Edition ISBN
Year Publisher
Text-Books
S11025-TB1
S11025-TB2
Reference-Books
Economics
S11025-RB1
Begg David, Stanley Fischer and Rudiger Dornbusch
S11025-RB2
CD / DVD
S11025-CD1
S11025-CD2
Web Links
S11025-WL1
S11025-WL2
7th 0077099478
2003 McGraw Hill
END OF DOCUMENT
Syllabus For V49: PG DIP (BIO-INF.)
Page 34