Introduction to Bioinformatics

disturbedtonganeseΒιοτεχνολογία

2 Οκτ 2013 (πριν από 3 χρόνια και 6 μήνες)

54 εμφανίσεις

Ayesha
Masrur

Khan

9
th

Feb, 2012

Course Outline

Introduction to Bioinformatics


Definition of Bioinformatics and Related Fields


Earliest Bioinformatics Efforts


Objective and Scope of Bioinformatics


Kind of Data Used in Bioinformatics


Introduction to Databases


Major Biological Databases

Sequence Alignment


Pairwise

Sequence Alignment


Database Similarity Searching


Multiple Sequence Alignment


Profiles and Hidden Markov Models


Protein Motifs and Domain prediction

2

Introduction

Course Outline..contd.

Gene and Promoter Prediction


Gene Prediction


Methods of Gene Prediction


Gene Prediction tools


Promoter and Regulatory Element Prediction


Promoter and Regulatory Element Prediction Tools


Structural Bioinformatics


Protein Structure Basics


Protein Structure Visualization, Comparison and Classification


Protein Structure Visualization Tools


Protein Secondary Structure Prediction


Protein Tertiary Structure Prediction


Protein Structure Prediction Tools


RNA Structure Prediction Methods and Tools

3

Introduction

Molecular
Phylogenetics


Phylogenetic

Basics


Phylogenetic

Tree Construction Methods and Programs


Phylogenetic

Tree Evaluation


Course Outline..contd.

Genomics and Proteomics


Introduction to Genomics


Tools for Genome Analysis


Genome Mapping, Assembly and Comparison


Functional Genomics


Introduction to Proteomics


Tools for Proteome Analysis


Advanced topics

Molecular dynamics simulation

Computational drug design

Microarray data analysis


4

Introduction

Recommended Books


Introduction to Bioinformatics, by T. K.
Attwood and D.J. Parry
-
Smith (2006) Pearson
Education, Ltd.
(available at the library, a few
copies will be made for your benefit)


Introduction to Bioinformatics: A Theoretical
and Practical Approach, by Stephen A.
Krawetz

and David D.
Womble
.


Essential Bioinformatics, by Jin
Xiong
(2006)
Cambridge University Press.



5

Introduction

Course Assessment

Assignment: 10%

Quizzes: 10 %

Sessional
-
1: 15 %

Sessional
-
2 (project

+ presentation)
: 20%

Terminal Exam: 45%


Note: Project

and assignments should be submitted on
the assigned due date. No late submissions or
extension requests will be accepted.


6

Introduction

Central Paradigm of Molecular Biology

DNA

RNA

Protein

Phenotype
(symptoms)

7

Introduction

Central Paradigm of Bioinformatics

8

Introduction

What is Bioinformatics?

Information technology applied to the management and
analysis of biological data
.

It was originally coined in the mid
-
1980s for the analysis of
biological data.


It

can

include

computational

manipulation

and

analysis

of

biological

sequence

data,

as

well

as

manipulation

and

analysis

of

three
-
dimensional

structural

data
.


What

laid

the

foundation

of

this

revolutionary

field?


Protein

sequencing

and

Nucleic

acid

sequencing

in

the

60
’s

and

70
’s

paved

the

way

for

sequence

revolution

and

hence

the

80
’s

saw

progress

in

computer
-
based

technologies

to

cope

with

this

surge

in

information


9

Introduction

Related fields

Systems Biology

Systems Biology: Studies the complex systems which exist within and across
multiple biological scales

10

Introduction

Structural Genomics: Pursuance of protein structures on a genome wide scale.

Proteomics: Study of the entire complement of proteins (proteome)

Genomics: Study of genomes of organisms.