Transcript Bioinformatics Study of Biology in post

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
biology and 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
bases
http://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
databases
-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-enzyme
http://www.biochem.ucl.ac.uk/bsm/dbbro
wser/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 recognition
http://www.bioinformaticssolutions.com/product
s/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 BLAST
http://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