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Introduction To Bioinformatics by Habeeb

Introduction to bioinformatics, basics of bioinformatics, concepts in bioinformatics, fundamentals of bioinformatics. Gives the basic idea on what bioinformatics is all about.

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Shaik Habeeb
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94 views

Introduction To Bioinformatics by Habeeb

Introduction to bioinformatics, basics of bioinformatics, concepts in bioinformatics, fundamentals of bioinformatics. Gives the basic idea on what bioinformatics is all about.

Uploaded by

Shaik Habeeb
Copyright
© Attribution Non-Commercial (BY-NC)
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
You are on page 1/ 36

INTRODUCTION TO

BIOINFORMATICS

HABEEB. SKM
DEPT OF BIOINFORMATICS
GURU NANAK COLLEGE
CHENNAI
Definition

What
Bioinformatics
Why

How

Tools & Databases

Basic protocol : Sequence Analysis

Sickle Cell Anemia

Drug Discovery & Bioinformatics


POLYPEPTIDE SYNTHESIS
Levels of Protein Structure
FUNCTIONS OF PROTEINS
Need for Bioinformatics
 Genomes are the complete set of chromosomes of
organism, which contain its full DNA, genes & lots of
“junk DNA”.

 Still a lot of genomes to be sequenced, considering the


1.8 million classified species, and the possibility of
existing 10 to 100 million unknown.

 Advanced Research Trends especially sequencing


genome projects have resulted in huge amounts of raw
data that must be stored, manipulated and analyzed.
 Narrow Definition:
 The use of computer tools to store, access and analyze nucleic acid data
and amino acid data and protein structure data.

 A broad Definition:
 The use of computer tools to store, access and analyze all types of
biological data.

 Personal Definition:
 The utilization of computation for biological investigation and
discovery—the process by which you unlock the biological world
through the use of computers.

 Data: text data, phylogenetic trees and metabolic maps


 Many applications in Biological Research, Drug design and Medicine
What is done in bioinformatics
 Bioinformatics is associated typically with massive
databases of gene and protein sequence and
structure/function information databases.

 Analysis and interpretation of various types of


biological data.

 Development of new algorithm and statistics with


which to assess biological information.
 Development and implementation of tools.
Role for Bioinformatics
Bioinformatics: Sequence Analysis

1. Start with unknown sequence

2. Find similar sequences

3. Create alignment

4. Create phylogenetic tree

5. Use information about knowns to make


predictions about unknown
RASMOL CN3D

GENBANK NEURAL
NETWORKS

DDBJ SWISSPDBVIEWER VMD


CHOU
FASMAN

EMBL
BL
TrEM
HMM GOR

UNIPROT

DATABASES & TOOLS


SWISSPROT
BLAST

FASTA

BLOSUM
CLUSTAL
AB INITIO KEGG
T-COFFEE METHOD
BRITE
PAM
IMGDB
THREADING
GONNET EXPASY

COG
HOMOLOGY
MODELING
PDB

PROSITE PFAM
SCOP

CATH
PHYLIP
ATLAS BLOCKS PRINTS
PAUP
Scoring Matrices: PAM & Blosum
HUMAN GENE MUTATION DATABASE (HGMD)
 These databases help us in carrying out our research.

 Huge amount of ever growing data.

 Numerous databases under same category to confirm predictions.

 Structure prediction with bioinformatics is so easy that it can be done in


few minutes to few hours.

 It’s a field with lots of potential to help research in diverse fields.

 Structural properties can easily be predicted.

 Many tools are available to understand the interaction between the target
protein and the ligand such as Autodock, iGemdock, Arguslab, Hex.

 Incase, the chemical structure of the ligand is not present in the chemical
structure databases it can be drawn using various structure drawing
softwares viz, ISIS Draw, Chemsketch.
A practical Approach:

Short DNA fragment: 10 20 30


0 GAGGAGAAGT CTGCCGTTAC TGCCCTGTGG
Six-frame translation:

Forward 0 : EEKSAVTALW Forward 1 : RRSLPLLPC

Forward 2 : GEVCRYCPV Reverse 0 : PQGSNGRLLL

Reverse 1 : HRAVTADFS Reverse 2 : TGQ!RQTSP

OWL Database Hits: 29

HBB2_PANLE HEMOGLOBIN BETA-2 CHAIN. - PANTHERA LEO


(LION).MW=15855.115900 LEN=146 Mol. wt. (calc) = 15855.1 Residues = 146

00 GHLTPEEKSAVTALWSKVNVDEVGGEALGR
31 LLVVYPWTQRFFESFGDLSTPDAVMGNPKV
61 KAHGKKVLGAFSDGLAHLDNLKGTFATLSE
91 LHCDKLHVDPENFRLLGNVLVCVLAHHFGK
121 E F T PPV QAAYQ K V VAG VANALAH KYH
Family Search Results

Scan Prosite

Pfam
Family Search Results contd:
Top 5 Fingerprint results with motifs
Alignment of Beta Hemoglobin entries of Printscan results:
Sickle cell anaemia- due to change in one base pair

CCTGATCC (Valine) – CCTGTTCC(Glutamine)


Phylogeny of HBB
What can we do with all this
Information?

 Better understand all organisms.

 Helps in disease diagnosis and prevention

 Helps understand our response to treatments, creating the possibility of


customized ones

 Identification of drug targets

 Gene Therapy

 More advances in specific treatment

 A better comprehension of our bodies

 A better comprehension of the relationships between organisms


Discover new drug targets—computational docking
HIV PROTEASE & INHIBITOR
Conclusion

 The recent enormous increase in biological data has made it necessary to


use computers, information technology to collect, organize, maintain, access
and analyze data.

 Computer speed, memory, exchange of information over the internet has greatly
facilitated bioinformatics.

 The bioinformatics tools available over the internet are accessible, well developed,
fairly comprehensive and relatively easy to use.
 You can reach me at:

 Email: [email protected]

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