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Bioinformatics Semester 8th
Bioinformatics Semester 8th
Bioinformatics Semester 8th
S c i e n c e
SyllabuS
a n d
Yashwantrao Chavan
Maharashtra
Open University
Dnyangangotri, Near Gangapur Dam,
Nashik 422 222, India
Phone: 0253-2231714, 2231715, 2231473
Fax: 2231473/ 2231716
Email: sctech@ycmou.com
Website: http://www.ycmou.com/
Te c h n o l o g y
S c h o o l
M.Sc.
in
Bio-Informatics
Page 1 of 14
Contents
1 Charts and Tables .............................................................................................................3
1.1 Bio-Informatics Programme Structure Charts ..............................................................3
1.2 Bio-Informatics Programmes Details ...........................................................................4
1.3 Bioinformatics Course Details ......................................................................................4
1.4 Course Distribution Chart ............................................................................................5
2 Syllabus ...........................................................................................................................6
2.1 Semester 08 ................................................................................................................6
Page 2 of 14
03
September
October
November
December
January
Course 1
4 CP, Theory
Course
Course 2
4 CP, Theory
Course
SBI012:
Communication
Skills
Course 3
4 CP, Theory
Course
Course 4
4 CP, Theory
Course
SBI014:
Environmental
Science
Course 5
4 CP, Practical or
Project-Work Course
SBI011:
Basic Biology
SBI031:
Basic
Biochemistry
SBI013:
Mathematics
SBI032:
General
Microbiology-I
SBI033:
Physiology
SBI034:
Metabolism
SBI015:
Lab Course
SBI035:
Lab Course
05
SBI051:
Basics of
Bioinformatics
SBI052:
Computer
Programming-I
SBI053:
DBMS-I
SBI054:
Introduction to
Molecular
Genetics
SBI055:
Lab Course
07
S08071:
Concepts in
Computing and
Basics of
Bioinformatics
SBI072:
Biological
Chemistry
SBI073:
Statistical
Techniques
SBI074:
Structural Biology
SBI075:
Lab Course
09
SBI093:
SBI094:
S09092:
Programming
Programming
SBI091:
Sequence-based Languages and
Languages and
Biochemistry of
Bioinformatics Softwarte Tools Softwarte Tools in
Metabolism
Approaches
in
Bioinformatics-II
Bioinformatics-I
SBI095:
Lab Course
March
April
May
June
July
Course 2
4 CP, Theory
Course
Course 3
4 CP, Theory
Course
SBI022:
Basic Chemistry
SBI023:
Applied Physics
Course 4
4 CP, Theory
Course
SBI024:
Programming
Concepts
Course 5
4 CP, Practical or
Project-Work Course
02
Course 1
4 CP, Theory
Course
SBI021:
Basic Statistics
04
SBI041:
Cell Biology-I
SBI042:
Basic Biosciences
SBI043:
Biophysical
Techniques-I
SBI044:
Molecular Biology-I
SBI045:
Lab Course
06
08
10
SBI061:
Computational
Molecular
Biology
SBI062:
Computer
Programming-II
SBI081:
Genomics
Databases and
Applications
SBI082:
Genetic
Information
Flow and
Processing
SBI101:
Genetic
Engineering
SBI102:
Genetics and
Genomics
SBI064:
Cell Biology,
Genetics &
Immunology
SBI084:
SBI083:
Protein Structure
Programming in
Prediction and
Perl
Molecular
Modeling
SBI103:
SBI104:
Database
Research
Management
Methodology
Systems
SBI063:
DBMS-II
SBI025:
Lab Course
SBI065
Lab Course
SBI085
Lab course
SBI105
Project
Page 3 of 14
Programme
M.Sc. (Bio-Informatics)
B.Sc. (Bio-Informatics)
TH: Theory
PR: Practical
Semester
Course
Code
CP
CST
SST
Marks
Cat
Type
SBI011
Basic Biology
40
120
100
BS
TH
SBI012
Communication Skill
40
120
100
BS
TH
SBI013
Mathematics
40
120
100
BS
TH
SBI014
Environmental Science
40
120
100
BS
TH
SBI015
Lab Course
80
120
100
BS
PR
SBI021
Basic Statistics
40
120
100
BS
TH
SBI022
Basic Chemistry
40
120
100
BS
TH
SBI023
Applied Physics
40
120
100
BS
TH
SBI024
Programming Concepts
40
120
100
BS
TH
10
SBI025
Lab Course
80
120
100
BS
PR
11
SBI031
Basic Biochemistry
40
120
100
DB
TH
SBI032
General Microbiology-I
40
120
100
DB
TH
SBI033
Physiology
40
120
100
DB
TH
SBI034
Metabolism
40
120
100
DB
TH
15
SBI035
Lab Course
80
120
100
DB
PR
16
SBI041
Cell Biology-I
40
120
100
DB
TH
SBI042
Basic Biosciences
40
120
100
DB
TH
SBI043
Biophysical Techniques-I
40
120
100
DB
TH
SBI044
Molecular Biology-I
40
120
100
DB
TH
20
SBI045
Lab Course
80
120
100
DB
PR
21
SBI051
Basics of Bioinformatics
40
120
100
DC
TH
SBI052
Computer Programming - I
40
120
100
DC
TH
SBI053
DBMS - I
40
120
100
DC
TH
SBI054
40
120
100
DC
TH
25
SBI055
Lab Course
80
120
100
DC
PR
26
SBI061
40
120
100
DC
TH
SBI062
Computer Programming - II
40
120
100
DC
TH
SBI063
DBMS - II
40
120
100
DC
TH
3
4
8
9
12
13
14
17
18
19
22
23
24
27
28
5
6
Name
Page 4 of 14
SN
Semester
Course
Code
29
Name
CP
CST
SST
Marks
Cat
Type
TH
SBI064
40
120
100
DC
30
SBI065
80
120
100
DC
PR
S08071
40
120
100
SC
TH
SBI072
Lab Course
Concepts in Computing and Basics
of Bioinformatics
Biological Chemistry
26
40
120
100
SC
TH
SBI073
Statistical Techniques
40
120
100
SC
TH
29
SBI074
Structural Biology
40
120
100
SC
TH
30
SBI075
Lab Course
80
120
100
SC
PR
26
SBI081
40
120
100
SC
TH
27
SBI082
40
120
100
SC
TH
SBI083
Programming in Perl
40
120
100
SC
TH
SBI084
40
120
100
SC
TH
30
SBI085
Lab Course
80
120
100
SC
PR
26
SBI091
Biochemistry of Metabolism
40
120
100
SC
TH
27
S09092
40
120
100
SC
TH
40
120
100
SC
TH
40
120
100
SC
TH
27
28
28
29
29
SBI094
30
SBI095
Sequence-based Bioinformatics
Approaches
Programming Languages and
Softwarte Tools in Bioinformatics-I
Programming Languages and
Softwarte Tools in Bioinformatics-II
Lab Course
80
120
100
SC
PR
26
SBI101
Genetic Engineering
40
120
100
SC
TH
27
SBI102
40
120
100
SC
TH
SBI103
40
120
100
SC
TH
SBI104
Research Methodology
40
120
100
SC
TH
SBI105
Project
80
120
100
SC
SP
28
28
29
10
30
SBI093
Course Category
No of
Courses
Credit
Points
% of Credit
Points
Counseling
Hours
% of
Counseling
Hours
10
40
20%
480
20%
10
40
20%
480
20%
10
40
20%
480
20%
20
80
40%
960
40%
Total
50
200
100%
2400
100%
No of
Courses
Credit
Points
% of Credit
Points
Counseling
Hours
% of
Counseling
Hours
67%
Course Type
TH: Theoretical
40
160
80%
1600
10
40
20%
800
33%
Total
50
200
100%
2400
100%
Page 5 of 14
Syllabus
2.1 Semester 08
2.1.1 SBI081
Code
Course Name
Prog
Sem
CP
CST
SST
Marks
Type
Cat
BI
40
120
100
TH
SC
Basic knowledge
databases
about
Remarks:
UN
Name of Unit
CST
Evaluation Pattern
10
10
10
10
UN
CP
Page 6 of 14
Details of
Chapters and Sections
Included in Syllabus
Edition Publisher,
Year
Price,
Order It Here
Text Books
SBI081-T1 Principles
of
Genome Included:
Analysis And Genomics (3rd Excluded:
Ed.) by Primrose, S.B. &
Twyman, R.M.
Blackwell
VCH
Publishing
Company, 2003.
Ram S. Verma
ISBN 1-56081-043-2.
Reference Books
SBI081-R1 Genome
mapping
sequencing
By
Dunham,
and
Ian
Horizon,
ISBN1-
898486-50-6.
Page 7 of 14
2.1.2 SBI082
Code
Course Name
SBI082 Genetic
Information
Processing
Flow
and
Course Prerequisites:
Prog
Sem
CP
CST
SST
Marks
Type
Cat
BI
40
120
100
TH
SC
Remarks:
UN
Name of Unit
CP
Gene Expression
Gene
Expression
Analysis
UN
and
Methods
of
CST
Evaluation Pattern
10
10
10
10
Gene Expression: Prokaryotic gene expression, operons positive & negative regulation, sigma
factors. Initiation, elongation and termination of transcription template & enzyme properties
Genes and Enzymes: Eukaryotic RNA polymerase I, II & III transcribed genes, promoter &
regulatory sequences, transcription factors, Techniques foot printing, Reporter genes
Genes RNA and Proteins: Organization of globin, immunoglobulin, HLA, r RNA and 5 sRNA
genes. Processing of RNA and Proteins Transport and Stability
Gene Expression and Methods of Analysis: Stress & hormones regulated gene expression
Organization of human genome. RFLP, Fingerprinting. RAPDs, Microarrays, ESTs
Details of
Chapters and Sections
Included in Syllabus
Edition Publisher,
Year
Price,
Order It Here
Text Books
SBI082-T1 Handbook
of
Biology
Rapley, Walker
Molecular Included:
Excluded:
Humane Press
McGraw-Hill, 2004
Reference Books
SBI082-R1 Molecular Biology
and Biotechnology
Rapley,Walker
Panima
Jones
&
Bartlett
Publishers, 2007.
Page 8 of 14
2.1.3 SBI083
Code
Course Name
Knowledge
of
SBI062
SBI052,
Prog
Sem
CP
CST
SST
Marks
Type
Cat
BI
40
120
100
TH
SC
Remarks:
UN
Name of Unit
CP
Control
Structures
&
Regular
Expressions
CST
Evaluation Pattern
10
10
Formats
10
10
UN
1
Formats:
What Is a Format? 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
Page 9 of 14
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
Book Code Title,
Author,
ISBN of Original Edition
Details of
Chapters and Sections
Included in Syllabus
Edition Publisher,
Year
Price,
Order It Here
Text Books
SBI083-T1 Beginning
Perl
Bioinformatics
for Included:
Excluded:
O-Reilly
James Tisdall,
SBI083-T2 Developing
Bioinformatics
O-Reilly
Computer Skills
Cynthia
Gibas,
Per
Jambeck,
SBI083-T3 Programming the Perl DBI
Alligator
Descartes,
O-Reilly
Tim
Bunce,
Reference Books
SBI083-R1 Advanced Perl Programming
O-Reilly
Sriram Srinivasan
Page 10 of 14
2.1.4 SBI084
Code
Course Name
SBI084 Protein
Structure
Prediction
Prog
Sem
CP
CST
SST
Marks
Type
Cat
BI
40
120
100
TH
SC
&
Molecular Modeling
Course Prerequisites:
Knowledge of
SBI074
SBI051,
SBI071
Understanding
the
levels
of
structure
organization of macromolecules and related
methods of structure determination
Understand
the
interaction
between
macromolecules
Remarks:
UN
Name of Unit
CP
Protein Purification
Qualitative
and
Evaluation of Protein
Exploring proteins
UN
1
Quantitative
CST
Evaluation Pattern
10
10
10
10
Mass
spectroscopy
MALTDI-TOF,
peptide
mass
fingerprinting,
eman
degradation, protein sequencing, automated soild phase peptide synthesis, NMr spectroscopy.
3
Exploring proteins:
Databases:, NDB & CCSD
Calculation of conformational energy for bio-macromolecules
Molecular Mechanics & Molecular Dynamics of Oligopeptides, Proteins, Nucleotides and small
Molecules
Mechanics and dynamics of bio-macromolecules
Simulation of molecular mechanics and dynamics
Simulations of Free Energy changes
Force fields
Molecular interactions of
Protein Protein
Protein DNA
Protein carbohydrate
DNA small molecules etc.
Page 11 of 14
Metaservers
Tertiary structures of Proteins using homology modeling
Evaluation of structure using Procheck, ProsaII etc.
Databases & servers for modeling
Approaches based on Neural; networks, genetic algorithms & machine learning methods
Fold recognition, threading
Methods to predict three dimensional structures of nucleic acids, rRNA
CASP, CFASP experiments
Book Code Title,
Author,
ISBN of Original Edition
Details of
Chapters and Sections
Included in Syllabus
Edition Publisher,
Year
Price,
Order It Here
Text Books
SBI084-T1 Proteins:
And Included:
Properties Excluded:
Structure
Molecular
Creighton, T.E.
SBI084-T2 Protein
Folding,.
New
York.
W.
H.
Freeman and Company,
1992
structure
New
York.
W.
H.
Freeman and Company,
1996
Creighton,T.
SBI084-T3 Protein
prediction:
practical
Second New
York.
W.
H.
Edition Freeman and Company,
1993.
modelling:
and
applications
Leach. A. R.
Reference Books
SBI084-R1 Structural
Methods
Bioinformatics
of
Wiley-Liss, 2003.
biochemical
Analysis V. 44 by Philip E.
Bourne
(Editor),
Helge
Weissig (Editor)
Page 12 of 14
2.1.5 SBI085
Code
Course Name
Prog
Sem
CP
CST
SST
Marks
Type
Cat
BI
80
120
100
PR
SC
Course Prerequisites:
Course Objectives: After successful completion of this
Perform
practical
related
to
Genomic
databases, Structural Bioinformatics, GIFP and
Perl.
Special Note: Study Centers should conduct any 20 activities out of total 24 activities given in the
list. Students are expected to perform all activities mentioned in each experiment and maintain the upto-date journal and get certified from the lab instructor.
UN
1
Browsing Human genome data, OMIM, SNP databases to understand genetic and metabolic
disorders at least 2 each
Mining genomic data to identify genomic features: codon usage, repeats, reversals,
Homologous regions, operon structures, syntenic regions, horizontal gene transfer
10
11
12
13
14
15
16
17
18
19
20
Reading
Feature
table
and
extraction
of
sequence
position
and
feature
information
for
biomacromolecules.
21
22
23
24
Page 13 of 14
Details of
Chapters and Sections
Included in Syllabus
Edition Publisher,
Year
Price,
Order It Here
Text Books
SBI085-T1 Bioinformatics
A beginners Guide
Claverie, Notredame
Included:
Excluded:
Willey
O-Reilly.
Reference Books
SBI085-R1 Bioinformatics
C.S.V. Murthy
Himalaya
House
Publishing
Page 14 of 14