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BT2351

BIO INFORMATICS II

LTPC
3003

OBJECTIVES
At the end of the course the student would have gained knowledge in physical mapping
techniques, overview of various genomes, techniques applied in Proteomics & Genomics and
functional Genomics. This will be very useful in the area of vaccine design.
UNIT I

INTRODUCTION
Overview of Genomes of Bacteria , Archae and Eukaryota.

UNIT II

PHYSICAL MAPPING TECHNIQUES

Top down and bottom up approach; linking and jumping of clones; genome sequencing;
placing small fragments on map; STS assembly; gap closure; pooling strategies; cytogenetic
mapping techniques.
UNIT III

FUNCTIONAL GENOMICS

Gene finding; annotation; ORF and functional prediction; Substractive DNA library
screening; differential display and representational difference analysis; SAGE; TOGA
UNIT IV

PROTEOMICS TECHNIQUES

Protein level estimation; Edman protein microsequencing; protein cleavage; 2 D gel


electrophoresis; metabolic labeling; detection of proteins on SDS gels; pattern analysis; Mass
spectrometry- principles of MALDI-TOF; Tandem MS-MS; Peptide mass fingerprinting.
UNIT V STRUCTURE FUNCTION RELATIONSHIP OF PROTEINS
9
Post translational modification; protein-protein interactions; glycoprotein analysis;
phosphoprotein analysis. NMR and Crystallography of protein of elucidate protein structure,
protein structure by modelly.
TOTAL: 45
REFERENCES
1.

Cantor and Smith, Genomics. John Wiley & Sons, 1999.

2.

Pennington and Dunn, Proteomics, BIOS Scientific Publishers, 2001

3.

Liebler, Introduction to Proteomics, Humana Press, 2002

4.

Hunt and Livesey, Functional Genomics, Oxford University press, 2000

ADDITIONAL REFERENCE BOOKS

1.

Primrose and Twyman, principles of genome analysis and genomics, Blacwell


Publishing Co., 2003
1

2.

Bioinformatics Methods and Applications- S.C. Rastogi- PHI Publication; 2005


DOC/LP/01/28.02.02

LP- BT 2351

LESSON PLAN

LP Rev. No: 00
Sub Code & Name: BT 2351
Unit: I
UNIT I

BIO INFORMATICS II

Branch: Biotechnology

Semester : VI

INTRODUCTION

Date:15/12/10
Page 1 of 6
6

Overview of Genomes of Bacteria , Archae and Eukaryota.

Session
No

1.

3.
5.
7.
8.
6.

Time
(min)

Topics to be covered
Introduction to Genomics,
Gene, Genome and
Organization of genes in
Prokaryotes

Text Book
&
Ref Book
AR1

50

Organization of genes in
Eukaryotes

50

Coding and Non coding


sequences, Higher order
structures
Genome relatedness- Sect-I

50
50

Genome relatedness- Sect II

50

Review

50

Page No
01-09
10-13
17-19

AR2

10-10
41-43

AR1

19-33

AR2

44-45

AR1

13-16

AR2

45-50

AR2

93-105

AR2

105-121
--

-----

Teaching
Method

BB&Chalk

BB&Chalk
BB&Chalk
BB&Chalk
BB&Chalk
BB&Chalk

DOC/LP/01/28.02.02

LP- BT 2351

LESSON PLAN
Sub Code & Name: BT 2351
Unit: I

BIO INFORMATICS II

Branch: Biotechnology

Semester : VI

LP Rev. No: 00
Date:15/12/10
Page 2 of 6

UNIT II

PHYSICAL MAPPING TECHNIQUES

Top down and bottom up approach; linking and jumping of clones; genome sequencing; placing
small fragments on map; STS assembly; gap closure; pooling strategies; cytogenetic mapping
techniques.

Session
No

Time
(min)

Topics to be covered

7.

Introduction to Genome mapping

50

8.

Genetic mapping and Linkage analysis

50

9.

Physical map- Cytogenetic map

50

10.
12.
13.
15.
16.

Physical map- STS assembly

50

Top down and bottom up approach,


Jumping of clones

50

Genome sequencing

50

Applications of Genetic maps


Gap closure

50
50

Text Book
&
Ref Book
ARB2
ARB2
ARB2

Page No
50-52
53-55
55-57

ARB2

57-60

ARB1
ARB2

47-70

ARB2

64-65

ARB1
ARB2
ARB2

71-78
65-66
68-70

60-63

Teaching
Method
BB& Chalk
OHP
BB& Chalk
OHP
BB& Chalk
OHP
BB& Chalk
OHP
BB& Chalk
OHP
BB& Chalk
OHP
BB& Chalk
BB& Chalk
OHP

ARB1
18.

Pooling strategies

50

ARB1

82-85
78-79

BB& Chalk

DOC/LP/01/28.02.02

LP- BT 2351

LESSON PLAN
Sub Code & Name: BT 2351
Unit: I

BIO INFORMATICS II

Branch: Biotechnology

Semester : VI

LP Rev. No: 00
Date:15/12/10
Page 3 of 6

UNIT III

FUNCTIONAL GENOMICS

Gene finding; annotation; ORF and functional prediction; Substractive DNA library
screening; differential display and representational difference analysis; SAGE; TOGA

Session
No

19.

Topics to be covered

Time
(min)

Gene finding; annotation,

Text Book
&
Ref Book
ARB2

50
ARB1

21.
22.
23.
24.

ORF and functional


prediction
Substractive DNA library
screening- Sect- I
Substractive DNA library
screening- Sect- II
Substractive DNA library
screening- Sect- III

50

ARB2

50

R2

50

R2

50

R2

25.

Differential display

50

R2

26.

Representational difference

50

R2

Page No
171-174,
12, 366

Teaching
Method

BB&Chalk

94-112
69-70
180-181
9-17
18-25
26-30
33-42
45-50

BB& Chalk
OHP
BB& Chalk
OHP
BB&Chalk
BB& Chalk
OHP
BB& Chalk
OHP
BB& Chalk

27.
28.
29.
30.

analysis- Sect- I
Representational difference
analysis- Sect- II
Representational difference
analysis- Sect- III
Representational difference
analysis- Sect- IV
TOGA, SAGE,

50

R2

50-70

50

R2

71-75

50

R2

75-80

50

ARB2

203-208

BB& Chalk
BB& Chalk
BB& Chalk
BB& Chalk

DOC/LP/01/28.02.02

LP- BT 2351

LESSON PLAN
Sub Code & Name: BT 2351
Unit: I

BIO INFORMATICS II

Branch: Biotechnology

Semester : VI

LP Rev. No: 00
Date:15/12/10
Page 4 of 6

UNIT IV PROTEOMICS TECHNIQUES

Protein level estimation; Edman protein microsequencing; protein cleavage; 2 D gel


electrophoresis; metabolic labeling; detection of proteins on SDS gels; pattern analysis; Mass
spectrometry- principles of MALDI-TOF; Tandem MS-MS; Peptide mass fingerprinting.

Session
No

Topics to be covered

Time
(min)

Text Book
&
Ref Book
Internet
sources

Page No

BB&Chalk

31.

Protein level estimation

50

32.

2 D gel electrophoresis

50

R2

181-186

BB & Chalk
OHP

33.

Detection of proteins on SDS gelsMetabolic labeling and pattern


analysis

50

R2

187-195

BB & Chalk
OHP

--------

Teaching
Method

BB & Chalk
OHP
BB & Chalk
OHP

34.

Edman protein microsequencing

50

R2

197-210-

35.

Protein cleavage

50

R2

210-218

50

R2

218-226

BB&Chalk

50

R2

227-234

BB&Chalk

50

R2

36.
37.
38.

Mass spectrometry- Peptide mass


fingerprinting, principles of
MALDI-TOF
Electrospray ionization
Tandem MS-MS
Analysis of post translational
modifications

234-237

BB&Chalk

DOC/LP/01/28.02.02

LP- BT 2351

LESSON PLAN
Sub Code & Name: BT 2351
Unit: I

BIO INFORMATICS II

Branch: Biotechnology

Semester : VI

LP Rev. No: 00
Date:15/12/10
Page 5 of 6

UNIT V

PROTEIN PROFILING

12

Post translational modification; protein-protein interactions; glycoprotein analysis;


phosphoprotein analysis, NMR and Crystallography of protein of elucidate protein
structure, protein structure by modelle.

Session
No
39.
40.
41.
42.
43.
44.
45.
46.
47.
48.
49.

Post translational modification


Protein Protein interactions
Glycoprotein analysis- Sect I
Glycoprotein analysis- Sect II
Phosphoprotein analysis- Sec I
Phosphoprotein analysisSec II
NMR and Crystallography of
protein of elucidate protein
structure - Sec I
NMR and Crystallography of
protein of elucidate protein
structure - Sec II
protein structure by modelle.

50
50
50
50
50

Text Book
&
Ref Book
ARB2
ARB2
T2
T2
T2

50

T2

114-120

BB&Chalk

ARB3

141-142

BB&Chalk

ARB3

143-145

BB&Chalk

Review- I
Review-II

50
50

Topics to be covered

Time
(min)

Page No

Teaching
Method

286-289
282-284
257-263
263-271
107-114

BB&Chalk
BB&Chalk
BB&Chalk
BB&Chalk
BB&Chalk

50
50
50

Internet
sources
-------

BB&Chalk
----------

BB&Chalk
BB&Chalk

DOC/LP/01/28.02.02

LP- BT 2351

LESSON PLAN
Sub Code & Name: BT 2351
Unit: I

LP Rev. No: 00

BIO INFORMATICS II

Branch: Biotechnology

Date:15/12/10

Semester : VI

Page 6 of 6
COURSE DELIVERY PLAN:
WEEK
UNITS

2
I Unit

II Unit

10

III Unit

11

12

VI Unit

13

14
V Unit

REFERENCES
1.

Cantor and Smith, Genomics. John Wiley & Sons, 1999.

2.

Hunt and Livesey, Functional Genomics, Oxford University press, 2000

3.

Liebler, Introduction to Proteomics, Humana Press, 2002.

4.

Pennington and Dunn, Proteomics, BIOS Scientific Publishers, 2001

ADDITIONAL REFERENCE BOOKS

1.

Primrose and Twyman, principles of genome analysis and genomics, Blacwell


Publishing Co., 2003

2.
3.

Bioinformatics Methods and Applications- S.C. Rastogi- PHI Publication; 2005.


Principles of biochemistry - Life at the Molecular Level By Donald Voet, Judith
G. Voet, Charlotte W. Pratt; 2007

Prepared by

Approved by

15

Signature
Name
Designation
Date

S.Naga vignesh
Asst.Professor, Biotechnology

Prof. M.Sivanandham
HOD, Biotechnology