Sub Code & Name BT2301/ BIOINFORMATICS

websterhissBiotechnology

Oct 1, 2013 (4 years and 1 month ago)

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/28.02.02



OBJECTIVE:


At the end of this course, the students would have
learnt about tools used in
Bioinformatics & how to use them. This will facilitate the students to undertake projects
in the modern biology.



SCOPE:


Bioinformatics subject enlists the basics of computing concepts with knowledge of
databases and machine l
e
arning. This course

will help the student to take up advanced
courses in electives like Molecular modeling and Drug design, Genomics and Proteomics

and also for carrying project work
. At the industry level, students will gain knowledge
about the pattern ma
tching and construction of phylogenic trees. This course also focuses
about the
advanced topics in bioinformatics like microarray analysis and systems biology.




















LESSON PLAN

LP
-

BT
230
1

LP Rev. No: 0
2

Date:
29
-
06
-
12

Page 1 of
7


Sub Code & Name
BT
230
1
/
BIOINFORMATICS


Branch: BIOTECHNOLOGY Semester
: V

DOC/LP/0
2
/28.02.02


U
nit syllabus:
INTRODUCTION







9 hrs


Basic UNIX commands


telnet


ftp


protocols


hardware


topology
-
search engines


search algorithms



Perl Programming
.




Session

No


Topics to be covered


Time

(min)


Ref/Page Numbers


Teaching
Aids

1

Introduction to UNIX,
Basic UNIX
commands
.

50

Notes
, RB3 (45
-
130)

BB/OHP

2

T
elnet
, File Transfer Protocol

50

TB 2 (52
-
59
, 190
-
202
)

B
B/OHP

3

Computer Hardware, Topology
.

50

TB 1 (116
-
119, 120
-
123
)

LCD

4

Protocols

50

TB 1 (144
-
155)

LCD

5

S
earch engines

50

TB 1 (144
-
155
, 182
-
190
)
,
RB1(124
-
144
)

LCD

6

S
earch algorithms


50

TB 1 (166
-
168), RB1(145
-
148)

LCD

7

Perl Programming
-
basics & da
ta
types

50

RB2 (
29
-
55
)
, RB3 (329
-
33
9
)

LCD

8

Perl Programming
-
subroutines &
control flow structures

50

RB2 (
87
-
104
)

LCD

9

Tutorial


f




iCa








LESSON PLAN

LP
-

BT
230
1

LP Rev. No: 0
2

Date:
29
-
06
-
12

Page
2

of
7


Sub Code & Name
BT
2301
/
BIOINFORMATICS


Unit:

1

Branch: BIOTECHNOLOGY Semester
: V

DOC/LP/0
2
/28.02.02


Unit syllabus:
DATABASES








9 hrs

Data management


data life cycle


database technology


interfaces and
implementation


biological databases and

their uses



Session

No


Topics to be covered


Time

(min)


Ref/Page Numbers


Teaching
Aids

1

Data management
.

50

TB 1 (48
-
64)

BB/OHP

2

D
ata life cycle

50

TB 1 (66
-
75)

LCD

3

D
atabase technology

I

50

TB 1 (75
-
84)

LCD

4

D
atabase technology

II

50

TB 1 (8
4
-
93)

LCD

5

I
nterfaces
, Implementation

50

TB 1 (93
-
100)

LCD

6

Biological databases, Uses

50

TB 2 (29
-
55)

BB/OHP

7

Data Mining

50

TB1 (270
-
272)

LCD

8

Tutorial
-

I
I

50


LCD

9

CAT I


50

--

--










LESSON PLAN

LP
-

BT
2301

LP Rev. No: 0
2

Date:
29
-
06
-
12

Page
3

of
7


Sub Code
& Name
BT
2301
/
BIOINFORMATICS


Unit:

II

Branch: BIOTECHNOLOGY Semester
: V

DOC/LP/0
2
/28.02.02


Unit syllabus:
PATTERN MATCHING & MACHINE LEANING



9 hrs

Pair wise sequence alignment


local vs. gl
obal alignment


multiple sequence alignment


dot matrix analysis


substitution matrices


dynamic programming


Bayesian
methods


tools


BLAST


FASTA
-

machine learning


neural networks


statistical
methods


Hidden Markov models



Homology Modeling
.




Session

No


Topics to be covered


Time

(min)


Ref/Page Numbers


Teaching
Aids

1

Pair wise

sequence alignment, local vs. global
alignment,

multiple sequence alignment
.

50

TB 1 (305
-
310)
, RB1
(73
-
123)

BB/OHP

2

D
ot matrix analysis
, Substitution matric
es

50

TB 1 (3
10
-
312
, 313
-
316
)

BB/OHP

3

D
ynamic programming

50

TB 1 (3
17
-
320)

BB/OHP

4

Bayesian methods

50

TB 1 (3
20
-
324)

BB/OHP

5

T
ools


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LESSON PLAN

LP
-

BT
2301

LP Re
v. No: 0
2

Date:
29
-
06
-
12

Page
4

of
7


Sub Code & Name
BT
2301
/
BIOINFORMATICS


Unit:

III

Branch: BIOTECHNOLOGY Semester
: V

DOC/LP/0
2
/28.02.02


Unit syllabus:
PHYLOGENY







9 hrs

Introduction; mutations; irrelevant mutations; controls; mutations as a measure of time;
distances; reconstruction; d
istances between species; estimating time intervals from
distances




Session

No


Topics to be covered


Time

(min)


Ref/Page Numbers


Teaching
Aids

1

Introduction

50

TB 2 (97
-
102)
, RB1
(103
-
105)

LCD

2

M
utations; irrelevant mutations

50

TB 2 (
102
-
104)

BB
/OHP

3

M
utations as a measure of

time

50

TB 2 (
104
-
108)

BB/OHP

4

M
utations as a measure of

distance
,
reconstruction

50

TB 2 (
108
-
114
)

BB/OHP

5

M
utations as a measure of

distance between
species

50

TB 2 (
114
-
118)

BB/OHP

6

E
stimating time intervals from
distances

I,
distances II

50

TB 2 (
118
-
126)

BB/OHP

7

Methods of Phylogenetic Analysis, UPGMA
Problems

50

RB1 (105
-
119)

LCD

8

Tutorial


f
s




iCa

9

C䅔 䥉
















LESSON PLAN

LP
-

BT
2301

LP Rev. No: 0
2

Date:
29
-
06
-
12

Page
5
of
7


Sub Code &
Name
BT
2301
/
BIOINFORMATICS


Unit:

IV

Branch: BIOTECHNOLOGY Semester
: V

DOC/LP/0
2
/28.02.02



Unit syllabus:
ADVANCED TOPICS IN BIOINFORMATICS



9 hrs


Biomolecular and cellular computing


micro array analysis


systems bi
ology




Session

No


Topics to be covered


Time

(min)


Ref/Page Numbers


Teaching
Aids

1

Biomolecular and cellular computing

-

Introduction

50

TB 2 (189
-
199)
, RB1
(309
-
310)

BB/OHP

2

Biomolecular and cellular computing

-

Tools

50

TB 2 (189
-
199)
, RB1
(310
-
311)

LCD

3

Working with DNA
M
icroarrays

50

TB 2 (
165
-
175)
, RB1
(191
-
196)

LCD

4

Clustering

Gene Expression analysis
,
Applications of Microarray technology

50

TB 2 (
165
-
175)
, RB1
(197
-
2
05
)

LCD

5

SAGE, Protein Interaction Networks


RB1 (205
-
208, 282
-
284)

LCD

6

S
ystems biology

I

50

TB 2 (
123
-
161), TB1
(383
-
384)

BB/OHP

7

S
ystems biology

II

50

TB 2 (
123
-
161), RB1
(291
-
308)

LCD

8

Tutorial


s




iCa

9

C䅔 䥉f


















LESSON PLAN

LP
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BT
2301

LP Rev. No: 0
2

Date:
29
-
06
-
12

P
age
6

of
7


Sub Code & Name
BT
2301
/
BIOINFORMATICS


Unit:

V

Branch: BIOTECHNOLOGY Semester
: V



DOC/LP/0
2
/28.02.02






Course Delivery Plan:


WEEK


1

2

3

4

5

6

7

8

9

10

11

12

13

UNITS


I

II

III

IV

V



Textbooks:



1.

B. Bergeron, Bioin
formatics Computing, PHI, 2002
.

2.
Westhead, D.R., Parish, J.H., Twyman, R.M., Instant Notes In Bioinformatics
.


References
:

1
.


S. C. Rastogi, N. Mendiratta, P.Rastogi., Bioinformatics Methods and Applications,
Prentice Hall of India

2. James Tisdall, Beg
inning Perl for Bioinformatics, O’Reilly
, 2001

3. Cynthia Gibas, Per Jambeck, Developing Bionformatics Computer Skills, Oreilly,
2001






Prepared by

Approved by

Signature



Name

P. K. Praveen Kumar

Prof.

Sulochana Somasundaram

Designation

Asst. Profes
sor

Head of the Department

Date

30.06.12

30.06.12



LESSON PLAN

LP
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BT
2301

LP Rev. No: 0
2

Date:
29
-
06
-
12

Page 7 of 7


Sub Code & Name
BT
2301
/
BIOINFORMATICS



Branch: BIOTECHNOLOGY



Semester
: V