Still no participant
Still no reviews
Introduce students to the field of computational biology. To make them realize the importance of insilico databases and computational tools to understand biology in a better way.
. To be familiar with the basic concepts of Computational Biology and its significance in biological data analysis.
. Learn and able to employ various computational tools for modern day research.
Module-I : Computers in biology and medicine
1.1 Overview of biological databases,
1.2 nucleic acid & protein databases,
1.3 primary, secondary, functional, composite, structural classification of databases,
1.4Data access, retrieval and submission, limitations of existing databases
Practice 1: Demonstration of biological databases: NCBI, EMBL, Swissprot/TrEMBL, UniProt.
https://www.youtube.com/watch?v=Phxkg5H5Q6E
Practice 2: Data retrieval using Entrez and SRS.
http://vlab.amrita.edu/index.php?sub=3&brch=273&sim=1437&cnt=1
Module-II : Sequence Alignments
2.1 Local alignments, Global alignment,
2.2 Scoring matrices - PAM, BLOSUM, Gaps and penalties, Dot plots.
2.3 Dynamic programming approach: Needleman and Wunsch Algorithm, Smith and Waterman Algorithm,
2.4Hidden Markov Model,
2.5 Heuristic approach: BLAST, FASTA.
Practice 3: Pairwise Sequence Alignment using BLAST
http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1428&cnt=1
Practice 4: Aligning Multiple Sequences with CLUSTAL W
http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1438&cnt=1
Module III
3.1 Alignment, tree building and tree evaluation,
3.2 Comparison and application of Unweighted Pair Group Method with Arithmetic Mean (UPGMA),
3.3 Neighbour Joining (NJ), Maximum Parsimony (MP), Maximum Likelihood (ML) methods,
3.4 Software for Phylogenetic analysis.
Module-IV: Insilico Drug Design
3.1. Insilico Drug Design: Basic Concepts, importance and application
3.2. Molecular force fields and energy minimization
3.3. Molecular Dynamics Simulation methods
3.4. Methods of Insilico Drug Design: structure and ligand based drug design approach
Practice : structure based drug design: Molecular docking using Biovia
Module-V: Systems and Synthetic biology
4.1. Systems and Synthetic Biology : Basic Concepts, importance and application
4.2. Systems Modeling
4.3. Formulating and Simulating Network Models in Biology
4.4. Potential Hazards of Synthetic Biology
Module-VI: Bioinformatics in Genome sequencing
6.1 Whole Genome Assembly and challenges,
6.2 Sequencing and analysis of large genomes,
6.3 Gene prediction, Functional annotation,
6.4 Functional genomics case studies, visualization tools such as PyMol.
Practice 5: Identification of gene characteristics using ExPaSy tools
Practice 6: Visualization using PyMol
Module-VII : Biopython and It's application in Computational Biology
7.1. Biopython: Introduction, important features and application of biopython in computational biology
7.2. Create a simple sequence in Biopython for DNA, RNA and Protein Alphabets
7.3. Sequence Alignment Tools in Biopython
7.4. PDB Module of Biopython
Practice: Align nucleotide/protein sequences using tools available in biopython
https://www.tutorialspoint.com/biopython/biopython_sequence_alignments.htm
Text Books:
University Press, New Delhi, 2000.
Reference Books
Biological Databases, Classification and different types of Biological Database
https://www.youtube.com/watch?v=QjHKV2tkHSI
DNA and Protein sequence analysis, Pairwise and multiple sequence alignment
https://www.youtube.com/watch?v=YVGpn-XNb58
Protein structural analysis, protein structure modeling and prediction
https://www.youtube.com/watch?v=OEzVUrhtZ6s
Practice : Demonstration and usage of web resources: EMBL, GenBank, ENTREZ
Database Management Systems: Basic Concepts, importance and applicationhttps://www.youtube.com/watch?v=wR0jg0eQsZA
Practice : Retrieving sequence data from Entrez
http://vlab.amrita.edu/index.php?sub=3&brch=273&sim=1437&cnt=1
InSilico Drug Design: Basic Concepts, importance and application
https://www.youtube.com/watch?v=Bmco5vDm7YA https://www.youtube.com/watch?v=aNl7z0MOAVM&list=PLCrHV5bhSbP0gP08ooS3tuBlRsEfDNWLs&index=3
Molecular force fields and energy minimization
https://www.youtube.com/watch?v=lLFEqKl3sm4
Methods of InSilico Drug Design: structure and ligand based drug design approach
Practice : structure based drug design: Molecular docking using Biovia
Systems and Synthetic Biology : Basic Concepts, importance and application
https://www.youtube.com/watch?v=rD5uNAMbDaQ
Formulating and Simulating Network Models in Biology
https://www.youtube.com/watch?v=hGR_gJjRWsc
Potential Hazards of Synthetic Biology
https://www.youtube.com/watch?v=8DDgHq9ewOo
Practice: Mathematical modeling and simulating of Biochemical network
http://vlab.amrita.edu/index.php?sub=3&brch=276&sim=1457&cnt=1
Algorithms in Computational Biology: Algorithms and complexity, biological versus computer algorithms
https://www.youtube.com/watch?v=48Xr-H05raA&t=29s
Recursive algorithms, iterative versus recursive algorithms
Overview of algorithm design techniques: Dynamic programming
https://www.youtube.com/results?search_query=dynamic+programming+mit+
Markov Chains and Hidden Markov Models : Concept and application in computational biology
https://www.youtube.com/watch?v=d5NMrA2HkG4&list=PLUl4u3cNGP63uK-oWiLgO7LLJV6ZCWXac&index=10
Practice: Pairwise Sequence Alignment using BLAST
http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1428&cnt=1
Practice: Aligning Multiple Sequences with CLUSTAL W
http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1438&cnt=1
Biopython: Introduction, important features and application of biopython in computational biology
Create a simple sequence in Biopython for DNA, RNA and Protein Alphabets
https://www.youtube.com/watch?v=r66YCsA4YqM
PDB Module of Biopython
https://www.youtube.com/watch?v=GkadFs-igdQ&list=PLNj5Z_OpbXrIRz6H8iaBfVJyIkWplNb1D&index=24
Practice: Align nucleotide/protein sequences using tools available in biopython
https://www.tutorialspoint.com/biopython/biopython_sequence_alignments.htm
Biojava: Introduction, importance and application of Biojava to computational biology
https://www.youtube.com/watch?v=OxZ0NGYiVRo
Protein structure module of Biojava and its use in manipulating structure of protein
https://github.com/biojava/biojava-tutorial/blob/master/structure/img/4hhb_jmol.png
Genome and sequencing module of biojava and its application for analyzing sequence data
https://biojava.org/wiki/BioJava:CookBook3:FASTQ
Practice : Study of protein structure using biojava
https://github.com/biojava/biojava-tutorial/blob/master/structure/img/4hhb_jmol.png
Dr. Jyoti Prakash Rath is presently working as Assistant Professor (Botany), School of Applied Science, Centurion University of Technology and Management, Odisha (Bolangir campus). After earning his Bachelor’s degree in Botany and Master’s in LifeSciences, Dr. Rath moved to New Delhi for his higher studies and received his M.Phil.(Bioinformatics) from Jawaharlal Nehru University […]