Development of Bioinformatics and its application on Biotechnology

By Wong Tak Hong

What is Bioinformatics? (1)

Bioinformatics -use of computer to store, analysis

and manipulate biological information

What is Bioinformatics? (2)

-manage and manipulate sequence data-use that sequence data in the analyses of

gene, protein, and DNA function-designing novel and incisive algorithms-create new/maintain existing databases

of information-allowing open access to the records held

within them

Onset of Bioinformatics

-Huge advances in the fields of molecular biologyand genomics especially after Human Genome Project

-This cause massive amount of biological information available

Onset of Bioinformatics 2

What is developed?

-Biological databases are consistent data that are stored in a uniform and efficient manner

-These databases contain data from a broad spectrum of molecular biology area

-Primary databases contain -information and annotation of DNA protein

sequences

-DNA and protein structures and DNA and protein expression profiles

                                     

Genbank

-First database setup to store DNA sequence data, set up In 1982

-manage by National Centre Biotechnology Information

-currently holds about 17 billion bases from more than 100,000 organisms

-Each of the sequences are given an ID number for easy identification in the database

http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html

EMBL (European Molecular Biology Laboratory) Nucleotide Sequence Database

-a comprehensive database of DNA and RNA sequences

-manage by European Bioinformatics Institute (EBI)

-information collected from the scientific literature and patent applications

-supported by 17 countries in Western Europe -currently contains nearly more than 10 million

baseshttp://www.ebi.ac.uk/embl/

SwissProt:

-a database of protein sequence, function and structure

-manage by European Bioinformatics Institute -provides a high level of integration with other datab

ases -a very low level of redundancy (means less identical

sequences are present in the database)http://www.ebi.ac.uk/swissprot/

                                     

EC-ENZYME:

The 'ENZYME' data bank contains the following data for a characterized enzyme:

-EC number -Recommended name and Alternative names-Catalytic activity-Cofactors-Pointers to the SWISS-PROT entry that

correspond to the enzyme-diseases associated with a deficiency of the

enzyme

Website of EC-enzymehttp://www.biochem.ucl.ac.uk/bsm/db

browser/protocol/ecenzfrm.html

Protein Data Bank

-manage by Research Collaboratory for Structural Bioinformatics (RCSB)

-a collection of all publicly available 3D structures of proteins, nucleic acids, carbohydrates

-variety of other complexes experimentally determined by X-ray crystallography and NMR

http://www.rcsb.org/pdb/

How rapidly developed?

Structural Analysis

-DNA sequences that encode proteins with specific function

-Researchers predict the 3D structure using protein or molecular modeling

-Experimentally determined protein structures (templates) are used

-to predict the structure of another protein that has a similar amino acid sequence (target)

Algorithm

A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.

PROSPECT

-Protein Structure Prediction and Evaluation Computer Toolkit

-a protein-structure prediction system -It construct a 3-D model of proteins by protein threading- Protein threading Algorithms for protein fold recognitionhttp://www.bioinformaticssolutions.com/pro

ducts/prospect.php

Example of 3D-Protein Model

Advantages in Protein Modeling

-Examining a protein in 3D allows for greater understanding of protein functions

-providing a visual understanding that cannot always be conveyed through still photographs or descriptions

Homology and Similarity Tools

-Homology and Similarity Tools are use to analyses similarity between two sequence or structure

-the degree of similarity between two sequences can be measured

-applied in evolutionary studies

BLAST (Basic Local Alignment Search

Tool)

-homology and similarity tools-develop by NCBI -Search programs designed for the

Windows platform -used to perform fast similarity

searches for protein or DNA -users can retrieve results and format

their results in different format

Website for BLASThttp://www.ncbi.nlm.nih.gov/BLAST/

Molecular Medicine

-Most of the disease has a genetic component and environmental component

-we can search for the genes directly associated with different diseases

-begin to understand the molecular basis of these diseases more clearly

-better treatments, cures and even preventative tests to be developed

Phenylketonuria (PKU)

The PAH (phenylalanine hydroxylase) gene maps on chromosome 12

PAH

Personalized Medicine

-Development of the field of pharmacogenomics -study of how an individual's genetic inheritance

affects the body's response to drugs -At present, doctors have to use trial and error to

find the best drug to treat a particular patient-In the future, doctors will be able to analyze a

patient's genetic profile and prescribe the best available drug therapy and dosage from the beginning

Microbial genomic application

-MGP (Microbial Genome Project) to sequence genomes of bacteria

-useful in energy production, industrial processing and toxic waste reduction

-scientists can begin to understand these microbes at a very fundamental level

-isolate the genes that give them their unique abilities to survive under extreme conditions

Waste clean up

-Deinococcus radiodurans is known as the world's toughest bacteria

-the most radiation resistant organism known

-Scientists are interested in this organism because of its potential usefulness in cleaning up waste sites that contain radiation and toxic chemicals

Deinococcus radiodurans

Evolutionary studies

-sequencing of genomes from different organism

-evolutionary studies can be performed to determine the tree of life

-find last universal common ancestor

Evolutionary studies 2

Impact of Bioinformatics 1

-Bioinformatics leads to advances in understanding basic biological processes, treatment, and prevention of many genetic diseases

-Bioinformatics has transformed the discipline of biology from a purely lab-based science to an information science as well

Impact of Bioinformatics 2

-modern biology and related sciences are increasingly becoming dependent on Bioinformatics

-Thus, Bioinformatics exhibits great potential in the future development of science and technology