Course Objectives

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.

Course Outcomes

Course Syllabus

Module-I : Introduction to Computational Biology and Bioinformatics

1.1 Nature and scope of Computational Biology and Bioinformatics,

1.2 Basic algorithms in Computational Biology,

1.3 Introduction to sequence alignment (only general ideas, not algorithm) - Local and global,

1.4 pair wise and multiple, BLAST

Module-II : Biological Databases

2.1 Overview of biological databases, Types of Biological data- Genomic DNA, cDNA, rDNA, ESTs, GSSs,

2.2 primary, secondary, functional, composite, structural classification of databases, Nucleotide, Protein Sequence Databases, Literature Databases, Sequence motifs Databases, Composite Databases, Genome Databases,.

2.3 Dynamic programming approach: Needleman and Wunsch Algorithm, Smith and Waterman Algorithm,

2.4Genome Browsers,

2.5 Bioinformatics Database search engines: -Text-based search engines (Entrez, DBGET/LinkDB).

2.6 Data access, retrieval and submission

Practice 1: Demonstration of biological databases: NCBI, EMBL, Swissprot/TrEMBL, UniProt.

https://www.youtube.com/watch?v=Phxkg5H5Q6E

Module III Sequence Alignments

3.1 Alignment, Local alignment, Global alignment,

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.

Practice 2: Pairwise Sequence Alignment using BLAST and Aligning Multiple Sequences with CLUSTAL W

http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1428&cnt=1

http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1438&cnt=1

Module-IV: Bioinformatics in Genome sequencing

4.1 Whole Genome Assembly and challenges,

4.2 Sequencing and analysis of large genomes,

4.3 Gene prediction, Functional annotation,

4.4 Functional genomics case studies, visualization tools such as PyMol.

4.5 NGS data analysis, Concept of Big data analysis.

Practice 3: Identification of gene characteristics using ExPaSy tools and Visualization using PyMol

Module-V: Insilico Drug Design

5.1. Insilico Drug Design: Basic Concepts, importance and application

5.2. Molecular force fields and energy minimization

5.3. Molecular Dynamics Simulation methods

5.4. Methods of Insilico Drug Design: structure and ligand based drug design approach

Practice 4:  structure based drug design: Molecular docking

Module-VI : Biopython and It's application in Computational Biology

6.1. Biopython: Introduction, important features and application of biopython in computational biology

6.2. Create a simple sequence in Biopython for DNA, RNA and Protein Alphabets

6.3. Sequence Alignment Tools in Biopython

6.4. PDB Module of Biopython

Module VII. Biostatistical Methods:

7.1. Data, Types of Data and data Visualization, Data arrangement, data normalization, Tabulation, Sampling methods, concept of Parametric and non-parametric statistics,

7.2. Measures of central tendency: Mean, Mode & Median, Measures of dispersion: Mean deviations, coefficient of variance (CV), Standard deviations, skewness and kurtosis.

7.3. Test of hypothesis; Student t-test and paired t-test; chi square test; Probability distribution (normal, binominal and poison distributions), Simple Correlation and Regression,

7.4 Analysis of variance (ANOVA): one way and two-way classification

Practice 5: Calculate the Mean Median Mode, Standard deviation from the supplied data set

Practice 6:  Test the goodness of fit

Text Books:

• Introduction to bioinformatics by Teresa K. Attwood, David J. Parry-Smith,1999,Pearson Education.
• Arthur M.Lesk, Introduction to Bioinformatics, Oxford University Press, New Delhi, 2003.
• Higgins and W.Taylor (Eds), Bioinformatics-Sequence, Structure anddatabanks, Oxford University Press, New Delhi, 2000

Reference Books

1. Bioinformatics: Sequence and Genome Analysis by Mount D., 2004, Cold Spring Harbor Laboratory Press, New York.
2. Biological Sequence Analysis: Probabilistic models of protein and Nucleic acids by Durbin et al., 2007,Cambridge University Press.
3. Bioinformatics- a practical guide to the analysis of Genes and Proteins by Baxevanis,A.D. and Francis Ouellellette, B.F., 1998, John Wiley & Sons, UK.
4. Introduction to bioinformatics by Teresa K. Attwood, David J. Parry-Smith, 1999,Pearson Education.
5. Arthur M.Lesk, Introduction to Bioinformatics, Oxford University Press, New Delhi, 2003.
6. D.Higgins and W.Taylor (Eds), Bioinformatics-Sequence, Structure and databanks, Oxford University Press, New Delhi, 2000.

Session 1

Nature and Scope of Computational Biology and Bioinformatics

https://www.youtube.com/watch?v=W-Ov2cUaYQY

Session 2

Basic algorithms in Computational Biology, Introduction to sequence alignment (only general ideas, not algorithm) - Local and global

Biological Databases, Classification and different types of Biological Database
https://www.youtube.com/watch?v=QjHKV2tkHSI

Session 3

DNA and Protein sequence analysis, Pairwise and multiple sequence alignment, BLAST.
https://www.youtube.com/watch?v=YVGpn-XNb58

Session 4

Overview of biological databases, Types of Biological data- Genomic DNA, cDNA, rDNA, ESTs, GSSs

https://www.youtube.com/watch?v=-wlFNr2FDHc

Session 5

primary, secondary, functional, composite, structural classification of databases, Nucleotide, Protein Sequence Databases, Literature Databases, Sequence motifs Databases, Composite Databases, Genome Databases, Genome Browsers

https://www.youtube.com/watch?v=wR0jg0eQsZA

Session 6

Demonstration and usage of web resources: EMBL, GenBank, ENTREZ, Data access, retrieval and submission, 

https://www.youtube.com/watch?v=Phxkg5H5Q6E

Session 7

Practice 1: Demonstration of biological databases: NCBI, EMBL, Swissprot/TrEMBL, UniProt.

https://www.youtube.com/watch?v=Phxkg5H5Q6E

Session 8

Practice : Retrieving sequence data from Entrez
http://vlab.amrita.edu/index.php?sub=3&brch=273&sim=1437&cnt=1

session 10

Session 10

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

Session 12

Multiple sequence alignment, Alignment, tree building and tree evaluation

https://www.youtube.com/watch?v=Pq4Cy76zNew

Session 13

Comparison and application of Unweighted Pair Group Method with Arithmetic Mean (UPGMA), Neighbour Joining (NJ)

https://www.youtube.com/watch?v=J-RjA889SKY

Session 14

Software for Phylogenetic analysis

https://www.youtube.com/watch?v=u9YNvHaRI5A

Session 15

Practice : Pairwise Sequence Alignment using BLAST and Multiple Sequence Alignment with CLUSTAL W

https://www.youtube.com/watch?v=tq-bWYVnQCM

Session 16

Whole Genome Assembly and challenges

https://www.youtube.com/watch?v=SnerjqgWt8Q

Session 17

Sequencing and analysis of large genomes

https://www.youtube.com/watch?v=SnerjqgWt8Q

Session 18

Gene prediction, Functional annotation, Functional genomics case studies

https://www.youtube.com/watch?v=EuCH5mqRylE

Session 19

Visualization tools such as PyMol

https://www.youtube.com/watch?v=7cX5bVENWAE

Session 20

NGS data analysis, Concept of Big data analysis.

https://www.youtube.com/watch?v=l4BAfRekohk

Session 21

Practice 3: Identification of gene characteristics using ExPaSy tool

https://www.youtube.com/watch?v=BAb_73kdkXc

Session 22

Insilico Drug Design: Basic Concepts, importance and application

https://www.youtube.com/watch?v=ewERE8gpqBU

Session 23

Molecular force fields and energy minimization; Molecular Dynamics Simulation methods

https://www.youtube.com/watch?v=veBZYlD6AF4

Session 24

Methods of Insilico Drug Design: structure and ligand-based drug design approach.

https://www.youtube.com/watch?v=Sts6TDc-wz4

Session 25

Practice 4: Molecular docking

https://www.youtube.com/watch?v=Sts6TDc-wz4

Session 26

Biopython: Introduction, important features and application of biopython in computational biology

https://www.youtube.com/watch?v=r66YCsA4YqM

Session 27

Create a simple sequence in Biopython for DNA, RNA and Protein Alphabets
https://www.youtube.com/watch?v=r66YCsA4YqM

Session 28

Sequence Alignment Tools in Biopython
https://www.youtube.com/watch?v=MxZCwiKusdE

Session 29

PDB Module of Biopython

https://www.youtube.com/watch?v=GkadFs-igdQ&list=PLNj5Z_OpbXrIRz6H8iaBfVJyIkWplNb1D&index=24

Session 30

Cluster Analysis using Biopython
https://www.youtube.com/watch?v=1XqG0kaJVHY

Session 31

Practice: Align nucleotide/protein sequences using tools available in biopython
https://www.tutorialspoint.com/biopython/biopython_sequence_alignments.htm

Session 32

Data, Types of Data and data Visualization, Data arrangement, data normalization, Tabulation, Sampling methods, concept of Parametric and non-parametric statistics

https://www.youtube.com/watch?v=2D5PswC7JBc

Session 33

Measures of central tendency: Mean, Mode & Median, Measures of dispersion: Mean deviations, coefficient of variance (CV), Standard deviations, skewness and kurtosis

https://www.youtube.com/watch?v=5_TuK1yCPD4

Session 34

Test of hypothesis; Student t-test and paired t-test; chi square test; Probability distribution (normal, binominal and poison distributions), Simple Correlation and Regression

https://www.youtube.com/watch?v=LSIgQH06j74

Session 35

Analysis of variance (ANOVA): one way and two-way classification

https://www.youtube.com/watch?v=JIu2XZDaIEw

Session 37

Practice 5: Calculate the Mean Median Mode, Standard deviation from the supplied data set

https://www.youtube.com/watch?v=RALOqYe9JEI

Session 38

Practice 6:  Test the goodness of fit

https://www.youtube.com/watch?v=f53nXHoMXx4