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Overview of Bioinformatics
A/P Shoba Ranganathan
Justin Choo
National University of Singapore
A Tutorial on Bioinformatics
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/Science/Bioinform/feature01.html)
• Annotate -> store -> search/retrieve -> analyze -> visualize
• Nucleic acid sequence (genes and RNAs), protein sequence and structural information.
Sequencing Of SARS …
Photo above shows the sequencing area of the lab. Taken from http://www.bcgsc.ca/bioinfo/SARS/
Partial Sequence of SARS …
>gi|30248028|gb|AY274119.3| SARS coronavirus TOR2, complete genome ATATTAGGTTTTTACCTACCCAGGAAAAGCCAACCAACCTCGATCTCTTGTAGATCTGTTCTCTAAACGA ACTTTAAAATCTGTGTAGCTGTCGCTCGGCTGCATGCCTAGTGCACCTACGCAGTATAAACAATAATAAA TTTTACTGTCGTTGACAAGAAACGAGTAACTCGTCCCTCTTCTGCAGACTGCTTACGGTTTCGTCCGTGT TGCAGTCGATCATCAGCATACCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTTC TTGGTGTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTCCTTCAGGTTAGAGACGTGCTAGTGCG TGGCTTCGGGGACTCTGTGGAAGAGGCCCTATCGGAGGCACGTGAACACCTCAAAAATGGCACTTGTGGT CTAGTAGAGCTGGAAAAAGGCGTACTGCCCCAGCTTGAACAGCCCTATGTGTTCATTAAACGTTCTGATG CCTTAAGCACCAATCACGGCCACAAGGTCGTTGAGCTGGTTGCAGAAATGGACGGCATTCAGTACGGTCG TAGCGGTATAACACTGGGAGTACTCGTGCCACATGTGGGCGAAACCCCAATTGCATACCGCAATGTTCTT CTTCGTAAGAACGGTAATAAGGGAGCCGGTGGTCATAGCTATGGCATCGATCTAAAGTCTTATGACTTAG GTGACGAGCTTGGCACTGATCCCATTGAAGATTATGAACAAAACTGGAACACTAAGCATGGCAGTGGTGC ACTCCGTGAACTCACTCGTGAGCTCAATGGAGGTGCAGTCACTCGCTATGTCGACAACAATTTCTGTGGC CCAGATGGGTACCCTCTTGATTGCATCAAAGATTTTCTCGCACGCGCGGGCAAGTCAATGTGCACTCTTT CCGAACAACTTGATTACATCGAGTCGAAGAGAGGTGTCTACTGCTGCCGTGACCATGAGCATGAAATTGC CTGGTTCACTGAGCGCTCTGATAAGAGCTACGAGCACCAGACACCCTTCGAAATTAAGAGTGCCAAGAAA TTTGACACTTTCAAAGGGGAATGCCCAAAGTTTGTGTTTCCTCTTAACTCAAAAGTCAAAGTCATTCAAC CACGTGTTGAAAAGAAAAAGACTGAGGGTTTCATGGGGCGTATACGCTCTGTGTACCCTGTTGCATCTCC ACAGGAGTGTAACAATATGCACTTGTCTACCTTGATGAAATGTAATCATTGCGATGAAGTTTCATGGCAG ACGTGCGACTTTCTGAAAGCCACTTGTGAACATTGTGGCACTGAAAATTTAGTTATTGAAGGACCTACTA
. . . . . . . . . . . . . . .
The complete genome of SARS, obtained from http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?30248028:NCBI:4812069
Bioinformatics -Timeline1980
2005
2000
1990
1985
1995
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?).
Biological Databases
• Collect, organise and classify data
• Query the dataset
• Retrieve entries based on keyword search
GenbankPDBEMBL
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?
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?
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?
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/
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/
Careers in Bioinformatics
Genomics:• Genome sequencing of
– Bacteria, viruses
– Animals
– Plants• Comparative genomics• Annotation and
Mapping• Gene Discovery
Careers in Bioinformatics
Functional Genomics (Gene Expression and Regulation):• Control Regions
– Switches– Circuits– Bypass– Feedback loops
• Environmental Effects• Diseased States• Chemical Consequences
Careers in Bioinformatics
Pharmacogenomics:• SNPs
– Regional, ethnic variations
– Inheritance patterns
– Radiological/ecological modifications• Therapeutic target recognition• Correlation of drug and expression effects• Pathway Effects
Careers in Bioinformatics
Proteomics:• Protein Profiling
– Alternate splice variants
– Orphan genes
– Cryptic introns• Gene Therapy
Careers in Bioinformatics
Structural Genomics:• Experimental Protein structures
– Apo state
– Holo state
– Structural modifications• Membrane Proteins• Homology Modelling• Comparative Modelling
Careers in Bioinformatics
Drug and Vaccine Design:• Screening Natural Products
– Plants
– Fungi
– Bacteria• Chemicals • In silico modifications of ligands• Vaccine design and delivery
Job Sectors
Academia
Research Institutes
Biotechnology
Bioinformatics
Pharmaceutical
Agriculture
Biodiversity