BI Sem9

o f
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: 2231716
Email: sctech@ycmou.com
Website: http://www.ycmou.com/
Bio-Informatics Programme Curriculum
Te c h n o l o g y
Yashwantrao Chavan Mahara shtra Open University
S c h o o l
M.Sc.
in
Bio-Informatics
Page 1 of 15
Contents
1 Charts and Tables .............................................................................................................3
1.1 Bio-Informatics Programme Structure Charts ..............................................................3
1.1.1 For Odd Numbered Semesters ...............................................................................3
1.1.2 For Even Numbered Semesters ..............................................................................3
1.2 Bioinformatics Programmes Details .............................................................................4
1.3 Bioinformatics Course Details ......................................................................................4
1.4 Course Distribution Chart ............................................................................................5
1.4.1 As per Course Category .........................................................................................5
1.4.2 As per Course Type ................................................................................................5
2 Syllabus ...........................................................................................................................6
2.1 Semester 09 ................................................................................................................6
2.1.1 SBI091 ..................................................................................................................6
2.1.2 S09092 ..................................................................................................................8
ProSite, Prodom, Pfam, CDD, BLOCKS etc..........................................................................9
2.1.3 SBI093 ................................................................................................................10
2.1.4 SBI094 ................................................................................................................12
2.1.5 SBI095 ................................................................................................................14
15
2008, YCMOU. All Rights Reserved.
Price: Indian Rs 200/- or US$ 50/- only. Free Download of Internet Version.
Last Update: Tuesday, September 29, 2009
Printed By:
Publisher: Registrar, YCMOU, Nashik 422 222, India.
Page 2 of 15
1 Charts and Tables

1.1 Bio-Informatics Programme Structure Charts
1.1.1 For Odd Numbered Semesters
Mandatory
CS Month
Odd
Numbered
Semester
01
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
1.1.2 For Even Numbered Semesters

Mandatory
CS Month
Even
Numbered
Semester
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 15
1.2 Bioinformatics Programmes Details

SN
Programme
For certification, student must confirm to

specified certification eligibility criteria and
following
courses
specified
for
the
respective programme must be successfully
completed
Post-Graduate Degree Programme

1
M.Sc. (Bio-Informatics)
All 20 courses at semester 07 to 10
Graduate Degree Programme

1
B.Sc. (Bio-Informatics)
All 30 courses at semester 01 to 06
1.3 Bioinformatics Course Details

CP: Credit Points
CST: Counseling Session Time
SST: Self-Study Time
Cat: Course Category from the below:
BS: Basic Science (Sem 01-02)
DB: Discipline Basic (Sem 03-04)
DC: Discipline Core (Sem 05-06)
SC: Specialization Courses (Sem 0710)

Type: Course Type from the below:
TH: Theory
PR: Practical
SP: Seminar or Project-Work

SN
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
Introduction to Molecular Genetics
40
120
100
DC
TH
25
SBI055
Lab Course
80
120
100
DC
PR
26
SBI061
Computational Molecular Biology
40
120
100
DC
TH
3
4
8
9
12
13
14
17
18
19
22
23
24
Name
Page 4 of 15
SN
Semester
Course
Code
CP
CST
SST
Marks
Cat
Type
27
SBI062
Computer Programming - II
40
120
100
DC
TH
28
SBI063
DBMS - II
40
120
100
DC
TH
SBI064
Cell Biology, Genetics &

Immunology
40
120
100
DC
TH
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
Genomics Databases & Applications
40
120
100
SC
TH
27
SBI082
Genetic Information Flow and

Processing
40
120
100
SC
TH
SBI083
Programming in Perl
40
120
100
SC
TH
SBI084
Protein Structure Prediction &

Molecular Modelling
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
29
27
28
28
29
Name
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
SBI102
Genetics and Genomics
40
120
100
SC
TH
SBI103
Database Mnagement Systems
40
120
100
SC
TH
SBI104
Research Methodology
40
120
100
SC
TH
SBI105
Project
80
120
100
SC
SP
28
27
28
29
10
30
SBI093
1.4 Course Distribution Chart

1.4.1 As per Course Category
SN
Course Category
No of
Courses
Credit
Points
% of Credit
Points
Counseling
Hours
% of
Counseling
Hours
BS: Basic Science
10
40
20%
480
20%
DB: Discipline Basic
10
40
20%
480
20%
DC: Discipline Core
10
40
20%
480
20%
SC: Specialization Courses
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%
1.4.2 As per Course Type

SN
Course Type
TH: Theoretical
40
160
80%
1600
SB: Skill Based (PR and PW)
10
40
20%
800
33%
Total
50
200
100%
2400
100%
Page 5 of 15
Syllabus
2.1 Semester 09
2.1.1 SBI091
Code
Course Name
SBI091
Biochemistry of Metabolism
Course Prerequisites:
Prog
Sem
CP
CST
SST
Marks
Type
Cat
BI
40
120
100
TH
SC
Course Objectives: After successful completion of this

course, student should be able to
Use
metabolism
and
metabolic
pathways
available on the websites
Basic knowledge of biochemistry
Remarks:
UN
CP
Introduction to Enzymology
Metabolism & Metabolic Pathways
Catabolism
Carbohydrates
Bioenergetics
UN
1
Name of Unit
Breakdown
of
CST
Evaluation Pattern
10
1 SAQ & 1 LAQ (in End Exam) and 5 MCQs

(in Self-Test) will be asked on these units.
10

10

10

Detail Syllabus of the Unit

Introduction to Enzymology: a) Historical Aspects of Enzymology; b) Enzymes as biocatalysts;
c) Classification and Nomenclature of enzymes; d) Allosteric enzymes; e) Coenzymes and
Cofactors
Structure and Characteristics of enzymes : a) Chemical Composition of enzymes; b) Physical
and Chemical characteristics of enzymes ( pH, Temperature and others); c) Enzyme Specificity;
d) Active site concept, Action of enzymes (Lock-and-Key model, Induced-fit model); e) 3-D
structure of Chymotrypsin and Lysozymes
Metabolism and Metabolic Pathways : (A) Metabolism :- a) Basic Considerations
Terminology e.g., precursor, substrate, building blocks, metabolites like primary and secondary,
macromolecules, catabolism, anabolism, amphibolism and anaplerosis; b) Concept of
Gluconeogenesis; c) Biosynthesis of fatty acids; d) Biosynthesis of triglycerides;
e)
Biosynthesis of Phospholipids; f ) Synthesis of amino acids (outline); and g) De novo synthesis of
nucleotides (B) Metabolic Pathways :- Study of metabolic pathways using Public Domain
pathways like KEGG, Biocyc (Ecocyc, Metacyc etc.,) Cazy and some others as available on
Internet websites
Catabolic Breakdown of Carbohydrates : a) EMP pathway in details; b) HMP pathway in
details; c) Breakdown of Lipids i) -Oxidation of fatty acids (saturated and unsaturated), ii) Oxidation of fatty acids; iii) Ketogenesis, ketosis; d) Breakdown of Proteins i) Hydrolysis, ii)
De-amination, iii) Transamination, and iv) Decarboxylation of amino acids;
e) Krebs cycle in
details and reference to its amphibolic and anaplerotic nature
Bioenergetics : a) Thermodynamics Concept of free energy, entropy, enthalpy, and redox
potential; b) Concept of high-energy bonds with examples like ATP, PEP, Fructose-1,6bisphosphate;
c)
Substrate-level
phosphorylation,
Electron-transport
chain,
Oxidative
phosphorylation; d) Photosynthesis i) Phototrophic Bacteria including Cyanobacteria, Pigments
involved in photosynthesis (chlorophylls, carotenoids, and phycobillins/phycobilliproteins, iii)
Cyclic and non-cyclic electron transfer associated with photophosphorylation, iv) Calvin cycle
Page 6 of 15
Book Code Title,

Author,
ISBN of Original
Edition
Text Books
SBI091-T1 Biochemistry
Keshav Trehan
Principles
SBI091-T2 Lehninger's
Biochemistry
D.L.Nelson and M.M.Cox
Details of
Chapters and Sections
Included in Syllabus
Edition
Year
Included: Enzymology
of Included:
Enzymology and metabolism
and other chapters
Biochemistry; Included:
SBI091-T3 Practical
Principles and Techniques
Enzymology
Keith
Wilson
and
John And metabolism and other
Walker
chapters
SBI091-T4 Principles of Biochemistry By All Chapters
D.J.Voet and J.W.Voet and
C.W.Pratt
st
SBI091-T5 Cell and Molecular Biology; 1 Unit : Enzymology;
Concepts and Experiments 2nd Unit : Metabolism;
By Gerald Karp
4th
Unit,
Bioenergetics
:
Thermodynamics
1st Unit : Enzymology
SBI091-T6 Enzymes
Palmer
Reference Books
Publisher,
Price,
Order It Here
2005, 4th edn
Wiley
Publications
Freeman
Eastern
2000, 5th edn.
Cambridge Univ. Press
2006,
Internnal John Wiley and Sons
Students Version
3rd edn.
2008, 5th edn;
Wiley
International
Student Version
SBI091-R1 Biochemistry
Voet
J.L. Jain
SBI091-R3 Lippincott's Biochemistry :
Illustrated Review
Pamela C Champe, Richard
A. Harvey
J.M.
Berg,
J.L.
Timoczko,.Lubert Stryer
Included:
Excluded:
S. Chand
Included:
All Chapters
1994, 2nd edn
Lippincott Williams and

Wilkins
All chapters
2002
(International
edn)
W.H. Freeman and Co.,

N. Y.
Page 7 of 15
2.1.2 S09092
Code
Course Name
S09092
Sequence
Approaches
based
Bioinformatics
Prog
Sem
CP
CST
SST
Marks
Type
Cat
BI
40
120
100
TH
SC
Course Objectives: After successful completion of

Basic knowledge of biology and bio- this course, student should be able to
Analyse molecular sequence data using

informatics and primary databases
various
sequence-based
bioinformatics
approaches
Remarks:
UN
1
Name of Unit
Sequence
Alignment
CP
Algorithms
Scoring Matrices
2
UN
1
Database Search Algorithms
MSA and Molecular Phylogeny
Derived Databases
&
CST
Evaluation Pattern
10
1 SAQ & 1 LAQ (in End Exam) and 5

MCQs (in Self-Test) will be asked on these
units.
10

units.
10

units.
10

units.

Sequence Alignment Algorithms & Scoring Matrices: Dynamic programming: basics
Alignment as an optimisation problem, Break penalty (opening & extension), Alignment scores
& other statistics, Concept of randomization, Needleman & Wunsch algorithm, Algorithm
Scoring scheme. Breaks and break penalty, Statistics and significance of scores, Smith &
waterman algorithm. Concept of local alignments, Algorithm, Differences between S&W and
N&W algorithm
Implementation. Scoring
matrices, Concept
of
similarity
and
distance
matrices,
Scoring
matrices for Nucleic acids, Scoring matrices for proteins. PAM series of matrices: derivation,
BLOSUM series of matrices: derivation, Comparison of PAM & BLOSUM, Matrices based on
structural similarity: Risler & CSW, Use and Applications of matrices
2
Database Search Algorithms: Significance of DNA & protein searches

BLAST: Algorithm, use of various parameters, statistics, analysing results and applications
Various BLAST versions: BLASTP, BLASTN, BLSATX, TBLASTN, Phi-BLAST and PSI-BLAST
(algorithms, unique features, advantages & limitations)
FAST A: Algorithm, parameters, statistics, applications and interpretation of results
Multiple sequence Alignments and Molecular Phylogeny:

Algorithms
employing
dynamic,
heuristic,
iterative
methods,
ClustalW,
Statistics,
Interpretation of MSA results, Programs to analyse MSA outputs: variability analysis, sequence
logos etc., Applications of MSA
Molecular Phylogeny: Overview of molecular evolution, Concepts in phylogenetic analysis,
rooted and unrooted trees, gene & species tree, algorithms to generate trees, statistical
significance, Use of Phylip, Mega, Treeview etc.
4
Derived Databases: Introduction to derived databases

Understanding concepts: sequence-based patterns, motifs, domains and family
Derived databases: organisation, searching and applications of following
Page 8 of 15
ProSite, Prodom, Pfam, CDD, BLOCKS etc.

Book Code Title,
Author,
ISBN of Original Edition
Details of
Edition Publisher,
Year
Price,
Order It Here
Text Books
S09092
-T1
BAXEVANIS,
A.D.
& Included:
OUELLETTEE,
B,F.F.: Excluded:
Bioinformatics: a practical
guide to the analysis of
genes and proteins.
2002
9-814-12675-6
S09092
-T2
ATTWOOD, T.K & PARRYSMITH, D.J.: Introduction

to Bioinformatics. ,
2006
81-7758-278-X
2004
0-8796-712-1
Reference Books
S09092
-R1
Mount, David:
Bioinformatics:
sequence
and genome analysis.
Page 9 of 15
2.1.3 SBI093
Code
Course Name
SBI093
Programming
Languages
and
Software Tools in BioinformaticsI
Basic
knowledge
concepts
of
Prog
Sem
CP
CST
SST
Marks
Type
Cat
BI
40
120
100
TH
SC
Course
programming course,
Objectives: After successful completion of this

student should be able to
write and execute programmes in C
debug programs effectively
Remarks:
UN
Name of Unit
CP
Introduction
Languages
Operators
Control
Structures,
Derived Data Types
The C-Language The C pre-processor
UN
to
Programming
Pointers
and
CST
Evaluation Pattern
10

10

10

10

Introduction to Programming Languages : a) Data Types Fundamental Data types; b) Definition of

Octal and Hexadecimal Constants; c) Arrays and Strings; d) Enumeration Constants
Operators : a) Substitution Operators, Numeric Operator, Increment and Decrement Operators; b)

Comparison Operators, Boolean Logical Operators, Digital Logical Operators; c) Hypothetical Operator, c)
Explicit Data type Conversion the cast operator, the size-of operator; d) Priorities of Operators, Mixture of
different data types in expression
Control Structures, Pointers and Derived Data Types : a) Structures if structure, while structure,
for structure, switch/case structure, continue structure, goto structure, recursion; b) Pointers
Definition, Pointer Variables, Applications, Dynamic Memory Allocation Functions; c) Derived Data Types
Data Structures, Bit Fields, Unions, Definition of New data type: typedef
The C-Language The C pre-processor : a) Definition of Constants : The #define directive, File Inclusion :
The #include directive, Conditional compilation; b) Input / Output and Library Functions : Input / Output
Functions, Other Library Functions; c) The Structure of C Programmes : Functions, Arguments of the main
function; d) Applications : Simple Bioinformatics Programmes
Book Code
Title,
Author,
Details of
Edition
Year
Publisher,
Price,
Order It Here
Text Books
SBI093-T1
Complete paper
Let us C-
BPB Publications
Yashavant P.kanetkar
SBI093-T2
The
Programming
Complete paper
Language
Kernighan;
1988
Prentice Hall. ISBN

0-13-110362-8
Dennis
M.
Outline
of
Ritchie
SBI093-T3
Schaum's
Complete paper
McGraw-Hill
Complete paper
Tata-McGraw-Hill
Fundamentals of Computing
with C++
SBI093-T4
The complete reference to

C
Schildt
Page 10 of 15
Book Code
Title,
Author,
Details of
SBI093-T5
Computer programming C
Complete paper
Edition
Year
Publisher,
Price,
Order It Here
Prentice Hall.
V. Rajaraman
Reference Books
SBI093-R1
Beginners
Guide
to Complete paper
Application programming in
Khanna
book
publishing co.
C
R.P.Salaria
SBI093-R2
Programming in C
Complete paper
GalGotia
Kris Jamsa
Page 11 of 15
2.1.4 SBI094
Code
Course Name
SBI094
Programming
Languages
and
Software Tools in BioinformaticsII
Working of computers
Prog
Sem
CP
CST
SST
Marks
Type
Cat
BI
40
120
100
TH
SC
Course Objectives: After successful completion of this

course, student should be able to
make use of JAVA programming in various

applications of bioinformatics
Remarks:
UN
Name of Unit
CP
Introduction to JAVA Programming
Classes and Objects in JAVA
Interactive Graphics
JAVA Applications in Bioinformatics
UN
1
2
3
4
CST
Evaluation Pattern
10

10

10

10


Introduction to JAVA Programming : a) Object-oriented programming and JAVA; b) JAVA Basics
Working with Objects, Strings, variant, Constant, Arrays, Conditionals and Loops, Iterative Statements
Classes and Objects in JAVA : a) Creating Classes in JAVA and Applications e.g., Applets basics
Interactive Graphics : Interaction Devices and Techniques, Graphical User Interface design
Transformations, 3-D viewing
JAVA Applications in Bioinformatics : a) The BIOJAVA project; b) Visualization Tools for Bioinformatics
SWISS-PDB- Viewer, Webmol, Rasmol (Raswin), Protein-Explorer, Cn3-D, VMD, MOlMol, Midas Plus, Pymol,
Chime, Chimera etc
Book Code
Title,
Author,
Details of
Edition Publisher,
Year
Price,
Order It Here
Text Books
SBI094-T1
SBI094-T2
SBI094-T3
Fundamentals of Interactive Included:

Computer Graphics
Excluded:
J.D. Foley, A.Van Dam
Computer graphics
Interactive graphics
Haren Baker
Java application
Bioinformaticsconcepts,skills
S.
C.
McGraw-Hill
2006
Prentice-Hall
Applications
Rastogi,
of
India,
Pvt. Ltd
Namita
Mendiratta, Parag Rastogi

SBI094-T4
Bioinformatics:Databases,
Tools
and
Algorithms
Orptia
Basu,
simminder
Java application
2007
Oxford
university
press
kaur Thukral
Reference Books
SBI094-R1
SBI094-R2
Procedural
Elements
for
Computer Graphics David
F. Rogers
Computer
Graphics
A Interactive graphics
Programming
Approach
Steven Harringion
Prentice Hall.
Page 12 of 15
Book Code
SBI094-R3
SBI094-R4
Title,
Author,
The Complete
Reference to
Java
Schildt
Computer graphics
Pradeep Bhatia
Details of
Java basics
Interactive graphics
Edition Publisher,
Year
Price,
Order It Here
Tata MaGraw-Hill
I.K.International
Publishing house Pvt Ltd.
Page 13 of 15
2.1.5 SBI095
Code
Course Name
Prog
Sem
CP
CST
SST
Marks
BI
80
120
100
SBI095 Practical course
Type Cat
PR
SC
Course Objectives: After successful completion of
Knowledge
of
Biochemistry
of this course, student should be able to
Metabolism, Concepts in computer
write and execute programs in C and JAVA

program,
Programming
in
object
debug the programs

oriented
languages,
Computer
graphics and visualization
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
up-to-date journal and get certified from the lab instructor.
UN
1

Program to carry out basic arithmetic operations (+,-,*, /, %)
Program to print a series of odd/even numbers
Program to find the biggest of 2/3 numbers
Program to find whether a given number is prime or not
Arrange a series of numbers/strings in ascending/descending order
Program to check whether a string is palindrome or not
Program to find factorial of an integer
Program to find factorial of an integer using function recursion
To perform Global Alignment Of Two Different Sequence Using Needle and Wnsch Algorithm .
10
To Perform Local Alignment Of Two Different Sequence Using Smith

Waterman Algorithm.
11
To Perform Sequence Alignment of Two Different Sequence Using Various Scoring Matrices and
Combination of Penalty Value
12
To Use And Understand BLAST Series: BLASTN, BLASTP, BLASTX,

TBLASTN
13
To Use and Understand BLAST Series: PHI-BLAST, PSI-BLAST
14
To Perform FASTA Search for DNA And Protein Data.
15
To Perform Multiple Sequence Alignment Using Clustal W Series.
16
To Study The Phylip Phylogenetic Package .
17
To Study Molecular Phylogeny Using Distance Methods / Phenetic Approach.
18
To Study Molecular Phylogeny Using Parsimony Method / Character-based Methods
19
Web Site Navigation To PROSITE Database
20
To Study ProDom Database : Its Organization And Searches
21
To Study Web Site Navigation to Block Database
22
Write a Java program to displaying general form of a class.

Write a Java program to create child fram window from within an applet.
23
24
Write a Java program to create an applet that sets the forgroundand background colors and
outputs a string.
Page 14 of 15
Book Code Title,

Author,
Details of
Edition Publisher,
Year
Price,
Order It Here
Text Books
SBI095-T1
Procedural
Elements
Computer Graphics
David Rogers
for Included:
Excluded:
Tata Macgraw
Reference Books
SBI095-R1
Bioinformatics
Practical
Guide to analysis of Genes
& Proteins
Andreas Baxevanis
Willey Intersciences
Publications
Page 15 of 15

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Bio-Informatics Programme Curriculum

Yashwantrao Chavan Mahara shtra Open University

Bio-Informatics Programme Curriculum

1 Charts and Tables

1.1.2 For Even Numbered Semesters

Bio-Informatics Programme Curriculum

1.2 Bioinformatics Programmes Details

For certification, student must confirm to

Post-Graduate Degree Programme

All 20 courses at semester 07 to 10

Graduate Degree Programme

All 30 courses at semester 01 to 06

1.3 Bioinformatics Course Details

BS: Basic Science (Sem 01-02)

DB: Discipline Basic (Sem 03-04)

DC: Discipline Core (Sem 05-06)

SC: Specialization Courses (Sem 0710)

SP: Seminar or Project-Work

Introduction to Molecular Genetics

Computational Molecular Biology

Bio-Informatics Programme Curriculum

Cell Biology, Genetics &

Genomics Databases & Applications

Genetic Information Flow and

Protein Structure Prediction &

Genetics and Genomics

Database Mnagement Systems

1.4 Course Distribution Chart

BS: Basic Science

DB: Discipline Basic

DC: Discipline Core

SC: Specialization Courses

1.4.2 As per Course Type

SB: Skill Based (PR and PW)

Bio-Informatics Programme Curriculum

Course Objectives: After successful completion of this

Basic knowledge of biochemistry

Metabolism & Metabolic Pathways

1 SAQ & 1 LAQ (in End Exam) and 5 MCQs

1 SAQ & 1 LAQ (in End Exam) and 5 MCQs

1 SAQ & 1 LAQ (in End Exam) and 5 MCQs

1 SAQ & 1 LAQ (in End Exam) and 5 MCQs

Detail Syllabus of the Unit

Bio-Informatics Programme Curriculum

Book Code Title,

2005, 4th edn

2000, 5th edn.

Cambridge Univ. Press

1994, 2nd edn

Lippincott Williams and

W.H. Freeman and Co.,

Bio-Informatics Programme Curriculum

Course Objectives: After successful completion of

Analyse molecular sequence data using

Database Search Algorithms

MSA and Molecular Phylogeny

1 SAQ & 1 LAQ (in End Exam) and 5

1 SAQ & 1 LAQ (in End Exam) and 5

1 SAQ & 1 LAQ (in End Exam) and 5

1 SAQ & 1 LAQ (in End Exam) and 5

Detail Syllabus of the Unit

Database Search Algorithms: Significance of DNA & protein searches