Brochure
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- Definition of Databases
- Database Design
- Knowledge Discovery
- Biological Databases
- Take Home Key Points
- Practical -1: NCBI Nucleotide Database
- Practical-2: Protein Databank (PDB)
- Quiz 1
- Assignment 1
Quick Facts
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Medium of instructions
English
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Mode of learning
Self study
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Mode of Delivery
Video and Text Based
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Course and certificate fees
Fees information
₹ 499 ₹3,099
certificate availability
Yes
certificate providing authority
Udemy
The syllabus
Module 1 Databases
Module 2 Sequence Alignment
- What is Sequence Alignment?
- Some Important Terms
- Types of Sequence Alignment
- What is Algorithms?
- Dot Matrix Algorithm; How Does It Work?
- Dot Matrix Algorithm; How to Interpret The Results?
- Dot Matrix Algorithm; Identification of Repeat Sequences
- Dot Matrix Algorithm; Advantages Vs Disadvantages
- Practical-3: DotMatcher for Qualitative Comparison of Sequence
- Assignment 2
- Dynamic Programming Method: How Does It Work?
- How to Transform Scoring Matrix to Alignment?
- Dynamic Programming; Some Important Terms to Understand
- Comparison Between DotMatrix and Dynamic Programming
- Practical-4: Global Pairwise Sequence Alignment Using DNA Sequences
- Practical-5: Pairwise Sequence Alignment Using Protein
- Practical-6: Local Pairwise Sequence
- Assignment 3
- Introduction to Database Searching; BLAST
- Type of Algorithms
- How Does Word Algorithm Work? (Part-1)
- How Does Word Algorithm Work? (Part-2)
- A Important Term For Word Algorithm
- Important Statistical Values to Evaluate the BLAST Results
- Different Type of BLAST Associated with NCBI Databases
- Practical -7: How to Use BLAST Program
- Assignment 4
- Optional: How to Use PSI-BLAST
- Multiple Sequence Alignment; An Introduction
- Algorithms for Multiple Sequence Alignment
- Progressive Sequence Alignment Algorithm
- Tools for Multiple Sequence Alignment
- Practical -8: How to Use CLUSTAL-W
- Practical -9: How to Use T-COFFEE
- Assignment 5
- Quiz 2
Section 3 : Genomic Bioinformatics
- Introduction of Module 3
- What is DNA?
- Where Is Our DNA is Located?
- What Is Role of DNA?
- What Does Gene Have?
- Algorithms for Gene Prediction-1
- Algorithms for Gene Prediction-2
- GC-Bias and Test Code; An Ab-initio Type of Algorithm
- Introduction of Markov Model (Part-1)
- Introduction of Markov Model (Part-2)
- Machine Learning and Gene Prediction
- Practical-10: Prediction of Prokaryotic Gene
- Practical-10.1 Prediction of Prokaryotic Regulatory Elements
- Practical-11 Prediction of Eukaryotic Gene
- Assignment 6
- Assignment 7
- Quiz 3
Module 4 : Structural Bioinformatics
- What is Protein? (Part-1)
- What is Protein? (Part-2)
- Some Important Points
- Role of Amino Acids in 3D Structure
- Peptide Bond; A link between Amino Acids
- Secondary Structures of Proteins
- Double Bond like Character in Peptide Bond & Ramachandran Plot
- Forces Stabilizing The Protein Structure
- Practical 13: Visualization of Protein Structure in Pymol (Part-1)
- Why Protein Structure Prediction is So Important?
- Protein Secondary Structure Prediction Algorithms (Part-1)
- Protein Secondary Structure Prediction Algorithms (Part-2)
- Practical-15: Prediction of Globular Protein Secondary Structure
- Assignment 8
- Algorithm for Secondary Structure Prediction of Transmembrane Proteins
- Practical-16: Prediction of Transmembrane Helix Secondary Structure
- Assignment 9
- 3D Structure Prediction Algorithms
- Homology Based Algorithm (Part-1)
- Homology Based Algorithm (Part-2)
- Homology Based Algorithm (Part-3)
- Homology Based Algorithm (Part-4)
- Model Validation & Draw back of Homology Based Algorithm
- Practical-17: Prediction of 3D structure Using Homology Modeling (Mdeller)
- Assignment 10
- Threading Algorithm for 3D Structure Prediction
- Practical-18: Prediction of 3D structure Using Threading Technique (I-TASSER)
- Assignment 11
- (Optional) Practical-18.1: Use of InterPro
- (Optional) Practical 20: How to Perform Docking easily Using Vina
- (Optional) Practical-21: How to Analyze the Docking Data
- (Optional) Practical 3: ZINC Database for Drug Searching
- Quiz 4
- (Very Important) Practical Learn How to Use Alpha-Fold
- Update Another GOR-IV Server for Secondary Structure Predictions
Module 4 : Evolutionary Bioinformatics
- What is Evolution and Phylogenetics
- Some Important Terms To Understand Phylogenetic Tree
- Different Type of Phylogenetic Trees
- Steps To Construct Phylogenetic Tree
- Selection of Molecular Marker for Tree Construction
- Alignment for Tree Construction
- Evolutionary Model Selection
- Methods To Construct Tree
- Validation of Tree By Bootstrapping
- Practical -19: Building Phylogenetic Tree
- Assignment 12
- Quiz 5
Module 6 (Optional)
- Practical-22: How to Install Linux in Window for Bioinformatics Analysis
- Practical-23: How to Install Gromacs in Windows
- Practical-24: How to Download Chemsketch
- Practical-25: Ligand Drawing and Making of Ligand 3D Structure
Instructors
Dr Muhammad Dujana
Instructor
Freelancer
Ph.D
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