Opportunities in Bioinformatics

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Opportunities in Bioinformatics Presented By
Dr G. P. S. Raghava Co-ordinator, Bioinformatic
Centre IMTECH, Chandigarh Email
raghava_at_imtech.res.in Web http//imtech.res.in/ra
ghava/
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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)
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What is Bioinformatics

• Biocomputing Application of Computer in
  Biosciences
• Biocomputing started in 1960s
• Explosion of Genomic Data
• Access and Management of Data
• BiocomputingInformation Science
• Role of Internet in BI

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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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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!
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More About Bioinformatics
ProteinAnalysisProteomics
GenomeMapping
MultipleSequenceAlignment
DatabaseHomologySearching
3DModeling
Bio Informatics
HomologyModelingDocking
SequenceAnalysis
SampleRegistration Tracking
IntellectualPropertyAuditing
IntegratedDataRepositories
CommonVisualInterfaces
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Computational Biology in the High-Throughput Era

• The Genome and Beyond
• Scientific Challenges
• Algorithmic Challenges
• Computational Challenges

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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 ?

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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

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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

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Application of Bioinformatics

• Genome Annotation
• Protein Structure Prediction
• Proteomics
• DNA Chip technology
• Disease Diagnostics
• Fingerprinting Technique
• Drug/Vaccine Design

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Genome Annotation

• The Process of Adding Biology Information and
• Predictions to a Sequenced Genome Framework

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Protein Structures

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Protein Structure Prediction

• Experimental Techniques
• X-ray Crystallography
• NMR
• Limitations of Current Experimental Techniques
• Protein DataBank (PDB) -gt 17000 protein
  structures
• SwissProt -gt 90,000 proteins
• Non-Redudant (NR) -gt 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

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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-gtC)
• Matching in Genome/Proteome Databases

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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

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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

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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

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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

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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

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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

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History of Bioinformatics in India

• Biocomputing started in 1950s
• 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)

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Education in Bioinformatics

• Role of BICs 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
• RD Institutes
• Ph.D in Bioinformatics (IMT)

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Business Comparisons
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• 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

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• 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

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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
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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

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Bioinformatics at IMT, Chandigarhhttp//imtech.re
s.in/bic/ http//imtech.res.in/

• Mirror Sites (http//www.imtech.res.in/mirror_site
  s/)
• 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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THANK YOU!