Dr N A Ganai Professor

Centre of Animal Biotechnology

SKUAST-Kashmir

Contents Introduction to Bioinformatics

Complexity of life

Size of genome

Exponential growth in information generation

Why and how to handle this information

Definition of Bioinformatics? Data bases

Tools

Scope of Bioinformatics

Anticipated benefits

Ethical, Legal, and Social Issues

DNA is not merely a molecule with a pattern;

it is a code, a language, and an information

storage mechanism

Size of Human Genome Each cell carries: 3.2 billion base pairs

A code you need to write in 500 books, each book of 500 pages

Length of DNA in adult man:

The total length of DNA present in one adult human is calculated as: (length of 1 bp)(number of bp per cell)(number of cells in the body)

(0.34 × 10-9 m)(6 × 109)(1013)

2.0 × 1013 meters

That is the equivalent of nearly 70 trips from the earth to the sun and back.

Human Genome Project • HGP: International research effort

• Began 1990, completed 2003

• Biggest ever project in life sciences

• 20 labs participated world around

• Next steps for ~30,000 genes – Function and regulation of all genes

– Significance of variations between people

– Cures, therapies, “genomic healthcare”

From DNA to Cell Function

DNA sequence (split into genes)

Amino Acid Sequence

Protein

3D Structure

Protein Function

Cell Activity

codes for

folds into

dictates determines

has

Lecture 2

Genomics

Transcriptomics

Proteomics Metabolomics

Year Base Pairs Sequences 1982 680,338 606

1983 2,274,029 2,427

1984 3,368,765 4,175

1985 5,204,420 5,700

1986 9,615,371 9,978

1987 15,514,776 14,584

1988 23,800,000 20,579

1989 34,762,585 28,791

1990 49,179,285 39,533

1991 71,947,426 55,627

1992 101,008,486 78,608

1993 157,152,442 143,492

1994 217,102,462 215,273

1995 384,939,485 555,694

1996 651,972,984 1,021,211

1997 1,160,300,687 1,765,847

1998 2,008,761,784 2,837,897

1999 3,841,163,011 4,864,570

2000 11,101,066,288 10,106,023

2001 15,849,921,438 14,976,310

2002 28,507,990,166 22,318,883

2003 36,553,368,485 30,968,418

2004 44,575,745,176 40,604,319

2005 56,037,734,462 52,016,762

2006 69,019,290,705 64,893,747

2007 83,874,179,730 80,388,382

2008 99,116,431,942 98,868,465

Av. Growth in data generation :

5400 times per year

Exponential Growth in Biological Databases:

High throughput Technologies

PCR : by Kary Mullis 1983 - an employee of Cetus Corporation, a

biotechnology firm in California

Awarded the Nobel Prize for the discovery of PCR in 1993

Microarray Technology

Real-Time PCR

DNA Chips

Sequencing

Sanger method : 1975

Chain Termination Method

Maxam Gilbert : 1977

Chemical Modification Method

Next Generation: 1994 High Throughput

Parallel sequencing

Entire genome can be sequenced

in a matter of weeks

History of DNA Sequencing

Avery: Proposes DNA as ‘Genetic Material’

Watson & Crick: Double Helix Structure of DNA

Holley: Sequences Yeast tRNAAla

1870

1953

1940

1965

1970

1977

1980

1990

2002

Miescher: Discovers DNA

Wu: Sequences Cohesive End DNA

Sanger: Dideoxy Chain Termination

Gilbert: Chemical Degradation

Messing: M13 Cloning

Hood et al.: Partial Automation

• Cycle Sequencing

• Improved Sequencing Enzymes

• Improved Fluorescent Detection Schemes

1986

• Next Generation Sequencing

•Improved enzymes and chemistry

•Improved image processing

Adapted from Eric Green, NIH; Adapted from Messing & Llaca, PNAS (1998)

1

15

150

50,000

25,000

1,500

200,000

50,000,000

Efficiency

(bp/person/year)

15,000

100,000,000,000 2008

The Genome Sequence is at hand…so?

“The good news is that we have the human genome.

The bad news is it’s just a parts list”

• Gene number, exact locations, and functions

• Gene regulation

• DNA sequence organization

• Noncoding DNA types, amount, distribution, information content, and functions

• Coordination of gene expression, protein synthesis, and post-translational events

• Interaction of proteins in complex molecular machines

• Predicted vs experimentally determined gene function

• Evolutionary conservation among organisms

• Protein conservation (structure and function)

• Proteomes (total protein content and function) in organisms

• Correlation of SNPs (single-base DNA variations among individuals) with health and

disease

• Disease-susceptibility prediction based on gene sequence variation

• Genes involved in complex traits and multigene diseases

• Complex systems biology including microbial consortia useful for environmental

restoration

• Developmental genetics, genomics

What Next??? We need to know every part, its function

and application

What is Bioinformatics? The newest, fastest growing specialty

in the life sciences that integrates biotechnology and computer science.

Computers aid to collect, analyze, and interpret biological information at the molecular level.

Bioinformatics encompasses a set of software tools that aid in:

molecular sequence analysis,

structural analysis

functional analysis

of genes & genomes and their corresponding products

Understand a living cell and how it functions at molecular level

Develop data basses and computational tools

Tools are used to mine (analyze) databases to generate knowledge to better understand the living systems

Goal of Bioinformatics

Biological Data basses : Why Why?

Store all the data (information) related to Genomics, Transcriptomics,

preoteomics, Metabolomics in Data Bases

Make biological data available to scientists.

To make biological data available in computer-readable form.

Types of Databases

Primary Databases: Store raw DNA/RNA and protein data submitted by scientists

GenBank: by NCBI USA www.ncbi.nlm.nih.gov/genbank/

EMBL: European : www.ebi.ac.uk/embl/

DDBJ: Japan www.ddbj.nig.ac.jp/

PDB: Protein Data bank http://www.rcsb.org/pdb/home/home.do

Data Bases … cont. Secondary data bases: Contain computationally processed or

manually curetted information based on primary data bases. SWISS-Prot: Curetted protein data base www.ebi.ac.uk/swissprot

TrEMBL: Translated Nucleic acid sequences in EMBL

PIR: annotated protein sequences

UniProt: Combined database of SWISSProt, TrEMBL, PIR

Prosite PRINTS BLOCKS PFAM

Specialized Data bases :cater to a particular research interest

FlyBase HIV Sequence data base Ribosome data base OMIM Microarray Gene expression database ExPASY etc. etc.

We need Bioinformatics Tools…

To mine (analyze) databases to generate knowledge to

better understand the living systems

Search/compare databases

Sequence Analysis

Genomics

Phylogenics

Structure Prediction

Molecular Modelling

Microarrays

Packages, Misc Apps, Graphics, Scripts

Examples of Bioinformatics Tools

Database interfaces (Search Tools) Genbank/EMBL/DDBJ, Medline, SwissProt, PDB, …

Sequence alignment BLAST, FASTA (Fast All)

Multiple sequence alignment Clustal, MultAlin, DiAlign

Gene finding Genscan, GenomeScan, GeneMark, GRAIL

Protein Domain analysis and identification pfam, BLOCKS, ProDom,

Pattern Identification/Characterization Gibbs Sampler, AlignACE, MEME

Protein Folding prediction PredictProtein, SwissModeler

Five websites that all biologists should Bookmark

NCBI (The National Center for Biotechnology Information; http://www.ncbi.nlm.nih.gov/

EBI (The European Bioinformatics Institute) http://www.ebi.ac.uk/

The Canadian Bioinformatics Resource http://www.cbr.nrc.ca/

SwissProt/ExPASy (Swiss Bioinformatics Resource) http://expasy.cbr.nrc.ca/sprot/

PDB (The Protein Databank) http://www.rcsb.org/PDB/

Anticipated Benefits of

Genome Research & Bioinformatics

Molecular Medicine : Gene Testing ,

Pharmacogenomics

Gene Therapy

improve diagnosis of disease

detect genetic predispositions to disease

create drugs based on molecular information

use gene therapy and control systems as drugs

design “custom drugs” (pharmacogenomics) based on

individual genetic profiles

Microbial Genomics

rapidly detect and treat pathogens in clinical practice

develop new energy sources (biofuels)

monitor environments to detect pollutants

protect citizenry from biological and chemical warfare

clean up toxic waste safely and efficiently

DNA Identification (Forensics)

identify potential suspects whose DNA may

match evidence left at crime scenes

exonerate persons wrongly accused of

crimes

establish paternity and other family

relationships

identify endangered and protected species

as an aid to wildlife officials (could be

detect bacteria and other organisms that

may pollute air, water, soil, and food

match organ donors with recipients in

transplant programs

determine pedigree for seed or livestock

breeds

Benefits: …contined

Agriculture, Livestock Breeding, and

Bioprocessing

grow disease-, insect-, and drought-resistant crops

breed healthier, more productive, disease-resistant

farm animals

grow more nutritious produce

develop biopesticides

incorporate edible vaccines incorporated into food

products

develop new environmental cleanup uses for

plants like tobacco

Benefits …cont

.

ELSI: Ethical, Legal,

and Social Issues • Privacy and confidentiality of genetic information.

• Fairness in the use of genetic information by insurers, employers, courts, schools, adoption agencies, and the military, among others.

• Psychological impact, stigmatization, and discrimination due to an individual’s genetic differences.

• Reproductive issues including adequate and informed consent and

use of genetic information in reproductive decision making.

• Clinical issues including the education of doctors and other health-

service providers, people identified with genetic conditions, and the

general public about capabilities, limitations, and social risks; and

implementation of standards and quality-control measures.

Health and environmental issues concerning genetically modified foods

(GM) and microbes.

Commercialization of products including property rights (patents, copyrights, and trade secrets) and accessibility of data and materials.

Common Questions

of a Student of biology