Overview of Bioinformatics

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Overview of Bioinformatics
A Tutorial on Bioinformatics
A/P Shoba Ranganathan Justin Choo
National University of Singapore
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What is Bioinformatics ?

• Bioinformatics is the study of the information
  content and information flow in biological
  systems and processes.
• - Michael Liebman in Bioinformatics An
  Editorial Perspective (http//www.netsci.org/Scie
  nce/Bioinform/feature01.html)
• Annotate -gt store -gt search/retrieve -gt
  analyze -gt visualize
• Nucleic acid sequence (genes and RNAs),
  protein sequence and structural information.

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SARS Its Implication ...
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SARS - Bioinformatics In Action
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Sequencing Of SARS
Photo above shows the sequencing area of the lab.
Taken from http//www.bcgsc.ca/bioinfo/SARS/
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Partial Sequence of SARS

• gtgi30248028gbAY274119.3 SARS coronavirus
  TOR2, complete genome ATATTAGGTTTTTACCTACCCAGGAAAA
  GCCAACCAACCTCGATCTCTTGTAGATCTGTTCTCTAAACGA
  ACTTTAAAATCTGTGTAGCTGTCGCTCGGCTGCATGCCTAGTGCACCTAC
  GCAGTATAAACAATAATAAA TTTTACTGTCGTTGACAAGAAACGAGTAA
  CTCGTCCCTCTTCTGCAGACTGCTTACGGTTTCGTCCGTGT
  TGCAGTCGATCATCAGCATACCTAGGTTTCGTCCGGGTGTGACCGAAAGG
  TAAGATGGAGAGCCTTGTTC TTGGTGTCAACGAGAAAACACACGTCCAA
  CTCAGTTTGCCTGTCCTTCAGGTTAGAGACGTGCTAGTGCG
  TGGCTTCGGGGACTCTGTGGAAGAGGCCCTATCGGAGGCACGTGAACACC
  TCAAAAATGGCACTTGTGGT CTAGTAGAGCTGGAAAAAGGCGTACTGCC
  CCAGCTTGAACAGCCCTATGTGTTCATTAAACGTTCTGATG
  CCTTAAGCACCAATCACGGCCACAAGGTCGTTGAGCTGGTTGCAGAAATG
  GACGGCATTCAGTACGGTCG TAGCGGTATAACACTGGGAGTACTCGTGC
  CACATGTGGGCGAAACCCCAATTGCATACCGCAATGTTCTT
  CTTCGTAAGAACGGTAATAAGGGAGCCGGTGGTCATAGCTATGGCATCGA
  TCTAAAGTCTTATGACTTAG GTGACGAGCTTGGCACTGATCCCATTGAA
  GATTATGAACAAAACTGGAACACTAAGCATGGCAGTGGTGC
  ACTCCGTGAACTCACTCGTGAGCTCAATGGAGGTGCAGTCACTCGCTATG
  TCGACAACAATTTCTGTGGC CCAGATGGGTACCCTCTTGATTGCATCAA
  AGATTTTCTCGCACGCGCGGGCAAGTCAATGTGCACTCTTT
  CCGAACAACTTGATTACATCGAGTCGAAGAGAGGTGTCTACTGCTGCCGT
  GACCATGAGCATGAAATTGC CTGGTTCACTGAGCGCTCTGATAAGAGCT
  ACGAGCACCAGACACCCTTCGAAATTAAGAGTGCCAAGAAA
  TTTGACACTTTCAAAGGGGAATGCCCAAAGTTTGTGTTTCCTCTTAACTC
  AAAAGTCAAAGTCATTCAAC CACGTGTTGAAAAGAAAAAGACTGAGGGT
  TTCATGGGGCGTATACGCTCTGTGTACCCTGTTGCATCTCC
  ACAGGAGTGTAACAATATGCACTTGTCTACCTTGATGAAATGTAATCATT
  GCGATGAAGTTTCATGGCAG ACGTGCGACTTTCTGAAAGCCACTTGTGA
  ACATTGTGGCACTGAAAATTTAGTTATTGAAGGACCTACTA
• . . . . . . . . . . . . . . .

The complete genome of SARS, obtained from
http//www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?302
48028NCBI4812069
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Bioinformatics -Timeline

• Single Structures
• Modeling Geometry
• Forces Simulation
• Docking
• Sequences, Sequence-Structure Relationships
• Alignment
• Structure Prediction
• Fold recognition
• Genomics
• Dealing with many sequences
• Gene finding Genome Annotation
• Databases
• Integrative Analysis
• Expression Proteomics Data
• Data mining
• Simulation again(whole cells?).

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Biological Databases

• Collect, organise and classify data
• Query the dataset
• Retrieve entries based on keyword search

PDB
EMBL
Genbank
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Sequence Analysis Software

• What is the information contained in a biological
  sequence?
• How can we analyse it to gain knowledge?
• Does it contain any functional clues?

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Sequence Comparison

• How can we compare a given sequence to the
  millions in the database?
• Which ones are truly related by evolution?
• What can the study of related sequences tell us?

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Sequence Alignment

• After collecting a set of related sequences, how
  can we compare them as a set?
• How should we line up the sequences so that the
  most similar portions are together?
• What do we do with sequences of different
  lengths?

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Protein Structure

• The function of a protein is a consequence of its
  folded state Anfinsen, 1961
• The 3D fold of a protein is called its structure
• In 3D, the business end of the protein has
  contributions from different regions of its
  sequence

Picture taken from http//www.strgen.org/
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Visualization

• Using graphic tools to view structures
• Simple commands to analyse structures and active
  sites
• Different graphic representations and colouring
  schemes

Picture taken from http//www.nature.com/
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Careers in Bioinformatics

• Genomics
• Genome sequencing of
• Bacteria, viruses
• Animals
• Plants
• Comparative genomics
• Annotation and Mapping
• Gene Discovery

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Careers in Bioinformatics

• Functional Genomics (Gene Expression and
  Regulation)
• Control Regions
• Switches
• Circuits
• Bypass
• Feedback loops
• Environmental Effects
• Diseased States
• Chemical Consequences

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Careers in Bioinformatics

• Pharmacogenomics
• SNPs
• Regional, ethnic variations
• Inheritance patterns
• Radiological/ecological modifications
• Therapeutic target recognition
• Correlation of drug and expression effects
• Pathway Effects

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Careers in Bioinformatics

• Proteomics
• Protein Profiling
• Alternate splice variants
• Orphan genes
• Cryptic introns
• Gene Therapy

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Careers in Bioinformatics

• Structural Genomics
• Experimental Protein structures
• Apo state
• Holo state
• Structural modifications
• Membrane Proteins
• Homology Modelling
• Comparative Modelling

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Careers in Bioinformatics

• Drug and Vaccine Design
• Screening Natural Products
• Plants
• Fungi
• Bacteria
• Chemicals
• In silico modifications of ligands
• Vaccine design and delivery

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Job Sectors

• Academia
• Research Institutes
• Biotechnology
• Bioinformatics
• Pharmaceutical
• Agriculture
• Biodiversity

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The End