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Opportunities in Bioinformatics Presented By Dr G. P. S. Raghava Co-ordinator, Bioinformatic Centre IMTECH, Chandigarh Email: [email protected] Web: http://imtech.res.in/raghava/.

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slide1
Opportunities in Bioinformatics

Presented By

Dr G. P. S. Raghava

Co-ordinator, Bioinformatic Centre

IMTECH, Chandigarh

Email: [email protected]

Web: http://imtech.res.in/raghava/

slide2
What is Bioinformatics (BI) ?More About Bioinformatics Historical Background Media Hype & ConfusionImportant Applications of BIBioinformatics in India Demand of BI ProfessionalsHow to Enter in BI (Course & Degrees)
what is bioinformatics
What is Bioinformatics
  • Biocomputing: Application of Computer in Biosciences
  • Biocomputing started in 1960’s
  • Explosion of Genomic Data
  • Access and Management of Data
  • Biocomputing+Information Science
  • Role of Internet in BI
slide4
Core of Bioinformatics
  • Relationships between
  • sequence 3D structure protein functions
  • Properties and evolution of genes, genomes, proteins, metabolic pathways in cells
  • Use of this knowledge for prediction, modelling, and design

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slide5
The challenge

(Boguski, 1999)

In 1995, the number of genes in the database started to exceed the number of papers on molecular biology and genetics in the literature!

more about bioinformatics
More About Bioinformatics

GenomeMapping

ProteinAnalysisProteomics

MultipleSequenceAlignment

DatabaseHomologySearching

3DModeling

BioInformatics

HomologyModelingDocking

SequenceAnalysis

SampleRegistration &Tracking

IntellectualPropertyAuditing

IntegratedDataRepositories

CommonVisualInterfaces

computational biology in the high throughput era
Computational Biology in the High-Throughput Era

The Genome and Beyond

  • Scientific Challenges
  • Algorithmic Challenges
  • Computational Challenges
historical background
Historical Background
  • Life Science - young compared to physics and chemistry
  • 1953 Structure of DNA
  • 1960s Understanding of “code of life”
  • 1970s Genetic manipulation technology
  • 1980s Widespread innovation -biotechnology/genetic revolution
  • 1990s Human Genome Project
  • 2000s Structural Genomics ?
media hype and confusion
Media Hype and Confusion
  • Anybody can do BI
  • BI can do anything
  • Colleges/Courses/Training
  • No Quality Check
  • Limited Knowledge of Subject
  • More user than developer
why bioinformatcs is required
Why Bioinformatcs is Required
  • Data growth is exponential
  • Difficult to understand life without BI
  • Detection of new diseases
  • BI tools allow to save expr. Expend.
  • Rational Drug design
  • Computer-aided vaccine design
application of bioinformatics
Application of Bioinformatics
  • Genome Annotation
  • Protein Structure Prediction
  • Proteomics
  • DNA Chip technology
  • Disease Diagnostics
  • Fingerprinting Technique
  • Drug/Vaccine Design
genome annotation
Genome Annotation

The Process of Adding Biology Information and

Predictions to a Sequenced Genome Framework

protein structure prediction
Protein Structure Prediction
  • Experimental Techniques
    • X-ray Crystallography
    • NMR
  • Limitations of Current Experimental Techniques
    • Protein DataBank (PDB) -> 17000 protein structures
    • SwissProt -> 90,000 proteins
    • Non-Redudant (NR) -> 800,000 proteins
  • Importance of Structure Prediction
    • Fill gap between known sequence and structures
    • Protein Engg. To alter function of a protein
    • Rational Drug Design
traditional proteomics
Traditional Proteomics
  • 1D gel electrophoresis (SDS-PAGE)
  • 2D gel electrophoresis
  • Protein Chips
    • Chips coated with proteins/Antibodies
    • large scale version of ELISA
  • Mass Spectrometry
    • MALDI: Mass fingerprinting
    • Electrospray and tandem mass spectrometry
      • Sequencing of Peptides (N->C)
      • Matching in Genome/Proteome Databases
overview of 2d gel
Overview of 2D Gel
  • SDS-PAGE + Isoelectric focusing (IEF)
    • Gene Expression Studies
    • Medical Applications
    • Sample Experiments
  • Capturing and Analyzing Data
    • Image Acquistion
    • Image Sizing & Orientation
    • Spot Identification
    • Matching and Analysis
comparision matcing of gel images
Comparision/Matcing of Gel Images
  • Compare 2 gel images
    • Set X and y axis
    • Overlap matching spots
    • Compare intensity of spots
  • Scan against database
    • Compare query gel with all gels
    • Calculate similarity score
    • Sort based on score
mass fingerprinting
Mass Fingerprinting
  • Add protease (e.g. trypsin)
    • Get fragment size of peptides
  • Scan against peptides of a protein obtained theortically by that protease
  • Scan against all proteomes
differential proteomics fingerprints of disease
Normal Cells

Disease Cells

Differential Proteomics: Fingerprints of Disease
  • Phenotypic
  • Changes
  • Differential protein expression
  • Protein nitration patterns
  • Altered phosporylation
  • Altered glycosylation profiles
  • Utility
  • Target discovery
  • Disease pathways
  • Disease biomarkers
fingerprinting technique
Fingerprinting Technique
  • What is fingerprinting
    • It is technique to create specific pattern for a given organism/person
    • To compare pattern of query and target object
    • To create Phylogenetic tree/classification based on pattern
  • Type of Fingerprinting
    • DNA Fingerprinting
    • Mass/peptide fingerprinting
    • Properties based (Toxicity, classification)
    • Domain/conserved pattern fingerprinting
  • Common Applications
    • Paternity and Maternity
    • Criminal Identification and Forensics
    • Personal Identification
    • Classification/Identification of organisms
    • Classification of cells
drug design based on bioinformatics tools
Drug Design based on Bioinformatics Tools
  • Detect the Molecular Bases for Disease
    • Detection of drug binding site
    • Tailor drug to bind at that site
    • Protein modeling techniques
    • Traditional Method (brute force testing)
  • Rational drug design techniques
    • Screen likely compounds built
    • Modeling large number of compounds (automated)
    • Application of Artificial intelligence
    • Limitation of known structures
  • Search of Target protein
  • Search of Lead compound
history of bioinformatics in india
History of Bioinformatics in India
  • Biocomputing started in 1950’s
    • IISc Banglore (Prof G Ramachandran)
    • Mostly analysis of protein structure
  • Distributed information center (DIC)
    • DBT initiate 9 DICs during 1986-7
    • National Facilities (IMT,IISc,IARI,JNU,MKU)
    • Sub-DICs started (around 50)
    • Mirror sites in 1999 (IMT,Pune,JNU,IISc)
education in bioinformatics
Education in Bioinformatics
  • Role of BIC’s in education
    • Workshops, training, course etc started
    • Facilities/Infrastructure in BI
    • Advanced diploma in BI (Pune,JNU,MKU)
    • M.Sc. In bioinformatics
  • Private Sector
    • Number of courses initiated
    • Dedicated training centers
  • Universities
  • R&D Institutes
    • Ph.D in Bioinformatics (IMT)
business comparisons
Company

Revenues

IT Budget

Pct

Chase-Manhattan

16,431,000,000

1,800,000,000

10.95 %

AMR Corporation

17,753,000,000

1,368,000,000

7.71 %

Nation’s Bank

17,509,000,000

1,130,000,000

6.45 %

Sprint

14,235,000,000

873,000,000

6.13 %

IBM

75,947,000,000

4,400,000,000

5.79 %

MCI

18,500,000,000

1,000,000,000

5.41 %

Microsoft

11,360,000,000

510,000,000

4.49 %

United Parcel

22,400,000,000

1,000,000,000

4.46 %

Bristol-Myers Squibb

15,065,000,000

440,000,000

2.92 %

Pfizer

11,306,000,000

300,000,000

2.65 %

Pacific Gas & Electric

10,000,000,000

250,000,000

2.50 %

Wal-Mart

104,859,000,000

550,000,000

0.52 %

K-Mart

31,437,000,000

130,000,000

0.41 %

Business Comparisons
slide28
Typical BioinformaticsMulti-Disciplinary Training
  • Scientists
    • Biology, Molecular Genetics, Clinical Biochemistry, Protein Structure Chemistry
  • Mathematicians
    • Statistics, Algorithms, Image processing
  • Computer Scientists
    • Database, User Interface/Visualizations, Networking (Internets/Intranets), Instrument Control
slide29
Typical BioinformaticsMulti-Disciplinary Functions
  • Scientists
    • Experimental Design & Interpretation
    • Laboratory Protocols & Standards/Controls
  • Mathematicians
    • Analysis & Correlation of Data
    • Validation methodologies
  • Computer Scientists
    • Information Storage / Control Vocabulary
    • Data Mining
bioinformatics architecture
External

Public

Databases

External

Proprietary

Databases

Bioinformatics Architecture

Java & Desktop

Programs

Web

Browser

Users

Workstation

MS

Access

SharedAccessDatabases

Web

Server

NT

servers

ActiveServer

Livewire

CGI

Unix

servers

&

Specialized

Hardware

Proprietary

Internal

Databases

business opportunities in bi
Business Opportunities in BI
  • Software development
  • Web servers development
  • Train manpower in Field of BI
  • Database management
  • Rational Drug design
  • Develop Diagnostic kits
  • Assist user in Vaccine development
  • Consultant to Biotech Companies
bioinformatics at imt chandigarh http imtech res in bic http imtech res in
Bioinformatics at IMT, Chandigarhhttp://imtech.res.in/bic/ http://imtech.res.in/
  • Mirror Sites (http://www.imtech.res.in/mirror_sites/)
  • Public Domain Resources in Biology (www.imtech.res.in/)
  • IMTECH Library on Internet (/lib/)
  • Concept of vaccine design
  • Protein Structure Prediction (Olympic-2000)
  • Gene Prediction
  • Software for general use
    • GNU software
    • SUN Freeware
    • PostgreSQL
  • Site: http//:imtech.res.in/raghava/www.html
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