# Computational Biology and Data Analysis

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# Code(Credit) : CUTM1435(3-1-0)

## 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.

## Learning Outcomes

. 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.

## Course Syllabus

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.

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:

• 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

Biological Databases, Classification and different types of Biological Database

## Session 2

DNA and Protein sequence analysis, Pairwise and multiple sequence alignment

## Session 3

Protein structural analysis, protein structure modeling and prediction

## Session 4

Practice : Demonstration and usage of web resources: EMBL, GenBank, ENTREZ

## Session 5

Database Management Systems: Basic Concepts, importance and applicationhttps://www.youtube.com/watch?v=wR0jg0eQsZA

## Session 6

Database Models, relational database

## Session 8

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

## Session 10

Molecular force fields and energy minimization

## Session 13

Molecular Dynamics Simulation methods

## Session 15

Practice :  structure based drug design: Molecular docking using Biovia

## Session 16

Systems and Synthetic Biology : Basic Concepts, importance and application

## Session 18

Formulating and Simulating Network Models in Biology

## Session 19

Potential Hazards of Synthetic Biology

## Session 20

Practice:  Mathematical modeling and simulating of Biochemical network
http://vlab.amrita.edu/index.php?sub=3&brch=276&sim=1457&cnt=1

## Session 21

Algorithms in Computational Biology: Algorithms and complexity, biological versus computer algorithms

## Session 22

Recursive algorithms, iterative versus recursive algorithms

## Session 23

Overview of algorithm design techniques:  Dynamic programming

## Session 24

Markov Chains and Hidden Markov Models : Concept and application in computational biology

## Session 25

Practice: Pairwise Sequence Alignment using BLAST
http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1428&cnt=1

## Session 26

Practice: Aligning Multiple Sequences with CLUSTAL W
http://vlab.amrita.edu/index.php?sub=3&brch=274&sim=1438&cnt=1

## Session 27

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

## Session 28

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

## Session 29

Sequence Alignment Tools in Biopython

## Session 31

Cluster Analysis using Biopython

## Session 32

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

## Session 33

Biojava: Introduction, importance and application of Biojava to computational biology

## Session 34

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

## Session 35

Genome and sequencing module of biojava and its application for analyzing sequence data
https://biojava.org/wiki/BioJava:CookBook3:FASTQ

## Session 36

Practice :  Study of protein structure using biojava
https://github.com/biojava/biojava-tutorial/blob/master/structure/img/4hhb_jmol.png

### Jyoti Prakash Rath

##### Assistant Professor
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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 […]