Bioinformatics Study of Biology in post-genomic era

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Development of Bioinformatics and its application
on Biotechnology
By Wong Tak Hong
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What is Bioinformatics? (1)

• Bioinformatics
• -use of computer to store, analysis and
  manipulate biological information

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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

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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

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Onset of Bioinformatics 2
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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

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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

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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/

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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/

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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

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• Website of EC-enzyme
• http//www.biochem.ucl.ac.uk/bsm/dbbrowser/protoco
  l/ecenzfrm.html

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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/

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How rapidly developed?
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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)

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Algorithm

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

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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/products/pr
  ospect.php

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Example of 3D-Protein Model












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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

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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

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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

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• Website for BLAST
• http//www.ncbi.nlm.nih.gov/BLAST/

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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

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Phenylketonuria (PKU)

• The PAH
• (phenylalanine hydroxylase)
• gene maps
• on chromosome 12

PAH
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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

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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

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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

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Deinococcus radiodurans
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Evolutionary studies

• -sequencing of genomes from different organism
• -evolutionary studies can be performed to
  determine the tree of life
• -find last universal common ancestor

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Evolutionary studies 2
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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

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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