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BIF401 : Bioinformatics I

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Dr. Safee Ullah Choudhry
Korea Advanced Institute of Science and Technology (KAIST)

Course Contents

Background of Bioinformatics, Introduction to Bioinforamtics, Need for Bioinformatics - I, Need for Bioinformatics - II, Applications of Bioinformatics - I, Applications of Bioinformatics - II,Frontiers in Bioinformatics - I, Frontiers in Bioinformatics - II, Overview of Course Contents - I, Overview of Course Contents - II, Overview of Course Contents - III, Gene, mRNA and Protein Sequences,Transcription, Nucleotides, Translation, Amino Acids, Storage of Biological Sequence Information,Using Entrez,Using Uniprot,Comparing Sequences,Similarities and Differences in Sequences, Pairwise Sequence Alignment-I, Pairwise Sequence Alignment-II, Pairwise Sequence Alignment-III, Dot Plots, Example of Dot Plots, Identity vs. Similarity, Introduction to Alignment, Approaches, Why local alignments? ,Aligning In-dels, Aligning Mutations in Sequences,, Introduction to Dynamic Programming, Dynamic Programming - Essentials, Dynamic Programming Methodology, Needleman Wunsh Algorithm-I, Needleman Wunsh Algorithm-II, Needleman Wunsh Algorithm-III, Needleman Wunsh Algorithm-Example, Backtracking Alignments ,Revisiting Global and Local Alignments ,Overlap Matches ,Example of Overlap Matches, Moving From global to local alignment, Smith Waterman Algorithm, Example of Smith Waterman Algorithm, Repeated Alignments, Exmaple of repeated alignment, Review of Traceback Strategies for Global, Overlap, Local and Repeated Alignments, Introduction to Scoring Alignments,, Measuring alignments by scoring, Scoring matrices, Deriving scoring matrices, PAM Matrices, BLOSSUM Matrices, Introduction to Multiple Sequences Alignment, More on Multiple Sequence Alignment, Progressive Alignment for MSA, MSA Example, CLUSTAL, Introduction to BLAST - I, Introduction to BLAST - II, BLAST Algorithm, Types of BLAST ,Summary of BLAST, Introduction to FastA-I, Introduction to FastA-II, FASTA Algorithm, Types of FASTA, Summary of FASTA, Biological Databases and Portals, Expasy, Ensemble, Uniprot, SwissProt, Homology, Paralogy and Orthology, Review of Sequence Alignment, Molecular evolution and phylogeny, Evolution of sequences, Algorithm and examples, Introduce UPGMA, UPGMA Algorithm, Solve an example, Introduce other Phylogenetic Methods, Examples of Maximum Parsimony, DNA to RNA Sequences, Base Complementarity, Types of RNA and their Function, Significance of RNA Structures, RNA Folding, Energies of Folding, Calculating Energies of Folding - An Example, Types of RNA Secondary Structures - I, Types of RNA Secondary Structures - II, Types of RNA Secondary Structures - III, RNA Tertiary Structures, Circular Representation of RNA Structures, Experimental Methods for Determining RNA Strucutres, Strategies for RNA Structure Prediction, Dot Plots for RNA 2' Structure Prediction, Energy Based Methods, Zuker Algorithm, Example - Zuker Algorithm, Zuker Algorithm - Flowchart, Martinez Algorithm, Dynamic Programming Approaches, Nussinov -Jacobson Algorithm Overview, NJ Algorithm Flowchart, Example - Jacobson Algorithm, Score Calculations and Traceback, Comparison of Algorithms, Web Resources: RNA Bricks, Web resources: MFOLD, From DNA/RNA Sequences to Proteins, Coding of Amino Acids, Open Reading Frames, ORF Extraction – A Flowchart, Sequencing Proteins, Application of MS in sequencing, Techniques for MS Proteomics, Types of MS-based proteomics, Bottom Up Proteomics, Two Approaches for Bottom Up Proteomics, Top Down Proteomics, Protein Identification, Protein Ionization Techniques, MS1 and Intact Protein Mass, Scoring Intact Protein Mass, Protein Fragmentation Techniques, Tandem MS, Measuring Experimental Fragment's Mass, Calculating Theoretical Fragment's Mass, Peptide Sequence Tags, Extracting Peptide Sequence Tags, Using Peptide Sequence Tags in Protein Search, Scoring Peptide Sequence Tags, In silico Protein Fragmentation, In silico Fragment Comparison and Scoring, Protein Sequence Database Search Algorithm, Integrative Scoring Schemes, Large Scale Proteomics, Proteomics Data File Formats, RAW File Format, MGF File Format, Open MS Data, Formats, Online Proteomics Tools - Mascot, Online Proteomics Tools - ProSight PTM, Example Case Study - I, Example Case Study - II, Example Case Study - III, Example Case Study - IV, Example Case Study - V, Example Case Study - VI, Properties of Amino Acids - I, Properties of Amino Acids - II, Properties of Amino Acids - III, Properties of Amino Acids - IV, Properties of Amino Acids - V, Structural Traits of Amino Acids - I, Structural Traits of Amino Acids - II, Structural Traits of Amino Acids - III, Structural Traits of Amino Acids - IV, Introduction to Protein Folding, Importance of Protein Folding, Computing Protein Folding Possibilities, Process of Protein Folding, Models of Protein Folding, Protein Structures, Primary, Secondary, Tertiary and Quaternary Structures, Primary Structure of Proteins, Secondary Structures of Proteins - I, Secondary Structures of Proteins -II, Tertiary Structures of Proteins, Quaternary Structures of Proteins, Introduction to Protein Bond Angles, Ramachandran Plot, Structure Visualization - I, Structure Visualization - II, Experimental Determination of Protein Structure, Protein Data Bank, Visualization Techniques, Online Resources for Protein Visualization, Types of Protein Visualizations, Introduction to Energy of Protein Structures, Calculating Energies of Protein Structures, Structure Determination for Energy Calculations, Review of Experimental Structure Determination, Protein Structures - Alpha Helices I, Protein Structures - Alpha Helices II, Protein Structures - Beta Sheets I, Protein Structures - Beta Sheets II, Protein Structures - Loops I, Protein Structures - Loops II, Protein Structures - Coils,  Structure Classification - I,  Structure Classification - II, Examples of Protein Domains, CATH Classification, Classification Databases, Algorithms for Structure Classification, Protein Structure Comparison, Strategies for Structure Comparison - I, Strategies for Structure Comparison - II, Online Resources for Structure Comparison, Protein Structure Prediction, Predicting Secondary Structures, Introduction to Chou Fasman Algorithm, 2’ Structures in Chou Fasman Algorithm, Chou Fasman Algorithm - I, Chou Fasman Algorithm - II, Chou Fasman Algorithm - III, Chou Fasman Algorithm - IV, Chou Fasman Algorithm – Flowchart I, Chou Fasman Algorithm – Flowchart II, Chou Fasman Algorithm – Flowchart III, Chou Fasman Algorithm – Improvements, Summary of Visualization, Classification and Prediction, Introduction to Homology modelling, Need for Homology Modelling, Seven Steps to Homology Modelling - I, Seven Steps to Homology Modelling - II, Seven Steps to Homology Modelling - III, Algorithm And Examples, Fold Recognition/Threading I, Fold Recognition/Threading II, Fold Recognition/Threading III, Online Tools for Fold Recognition, iTASSER, GOR Algorithm, 3D-1D Bowie Algorithm, Example of 3D-1D Algorithm, Machine Learning Approaches to Structure, Prediction, Neural Networks for Structure Prediction, Introduction to Neural Networks I, Introduction to Neural Networks II, Application of Neural Networks for Structure Prediction, PSIPRED, Introduction to Hidden Markov Models, Application of Hidden Markov Models to Structure Prediction, Ab initio modelling, Hinds and Levitt Algorithm, Example of HL Algorithm, Computational Assesment of Structure Prediction (CASP), Summary of Homology Modelling, Online Tools for Homology Modelling, Databases for Structure Modelling, SWISS MODEL, Review of Structure Modelling, Example of Hepatitis C Virus genotype 3A Modelling - I, Example of Hepatitis C Virus genotype 3A Modelling - II