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Introduction to Computational Biology

Introduction to Computational Biology


Gagan Kumar Panigrahi


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Course Name : Introduction to Computational Biology

Code(Credit) : ABC01(3-1-0)

Course Description

Computational Biology is a multidisciplinary approach to applying data-scientific methods, processes, or theories to the study of biological systems. The field includes foundations in Genetics, Genomics, Evolution and related disciplines. The course essentially emphasizes on a variety of bio-computational approaches used to solve modern biological queries. This course comprises of a toolkit of existing software resources built on these computational approaches and that are used by thousands of biologists every day. Therory and Practice components of this course align with the fundamental concepts of computational biology.

Course Objectives

High-throughput technologies produce massive amounts of data, much too large to analyze by hand. The objective of this certificate course is to:
1. Analyze DNA, RNA, and protein sequences using computational tools.
2. Demystify computer science, molecular biology, and some of the ways they intersect.
3. Convert a biological question into a computational problem that can be solved using computational tools.

Learning Outcomes

At the end of this certificate course, learners are expected to learn:
1. About the properties of DNA, RNA, and proteins, the relationships among these molecules, and some biological questions that have puzzled researchers.
2. How to convert a biological question into a computational problem that can be solved using computational tools.
3. How to read and understand solutions to computational problems, which will be formalized as a series of tasks.
4. About general approaches for solving computational problems and learners will be able to apply these approaches to new problems they encounter.

Course Syllabus

Data bases in Bioinformatics: Introduction, Biological Databases, Classification format of Biological Database, Biological Database Retrieval System. NCBI: Tools and Databases of NCBI, Database Retrieval Tool, Sequence Submission to NCBI, Basic local alignment search tool (BLAST), Nucleotide Database, Protein Database, Gene Expression Database. EMBL: Introduction, Sequence Retrieval, Sequence Submission to EMBL, Sequence analysis tools. DDBJ: Introduction, Resources at DDBJ, Data Submission at DDBJ. PIR: About PIR, Resources of PIR, Databases of PIR, Data Retrieval inPIR. Swiss-Prot: Introduction and Salient Features.
Practice-I: Data retrieval using GenBank, SRS and DBGET
Practice-II: Sequence similarity using BLAST


Sequence Alignments: Introduction, Concept of Alignment, Multiple SequenceAlignment (MSA), MSA byCLUSTALW. Molecular Phylogeny:Methods of Phylogeny, Software for Phylogenetic Analyses, Consistency of Molecular Phylogenetic Prediction.
Practice-III:MSA using Clustal omega
Practice-IV: Phylogenetic analysis using MEGA

Module III

Applications of Bioinformatics: Structural Bioinformatics in Drug Discovery, Quantitative structure-activity relationship (QSAR) techniques in Drug Design, Microbial genome applications, Crop improvement, Bioinformatics in genome sequencing.
Practice-V: Molecular docking
Practice-VI: Gene prediction tools

Text Books:

1. Geoffrey M. Cooper, Robert E. Hausman (Boston University). The Cell: A Molecular Approach. ASM Press, Washington D.C. Fourth edition.
2. Cell and molecular biology Robertis, De and Robertis Lea and Febiger. Eighth Edition.

Reference Books:

1. Molecular Biology of the Cell Alberts, B., et al. 6th Rev ed. Taylor & Francis; 2014 ISBN 978-0-8153-4432-2 (hard), 978-0-8153-4524-4
2. Essential Cell Biology Alberts, B., et al. 4th Rev ed. Garland; 2013 ISBN 9780815344544
3. Lewin’s Genes XII Krebs, J.E. et al. Jones & Bartlett; 2018 ISBN 9781284104493
4. Molecular Cell Biology Lodish H. et al. 8th ed. W.H. Freeman and Company; 2016 ISBN 9781464183393

Session Plan

Session 1

Data bases in Bioinformatics

Session 2

Primary databases-Genomic: NCBI, EMBL, DDBJ

Session 3

Secondary databases- PDB, CSD, MMDB, SCOP, CATH

Session 4

Sequence motif databases- Prosite, ProDom, Pfam, Interpro

Session 5

Genome databases- Viral, Bacterial, organism specific

Session 6

Organism specific databases- OMIM, SGD, TAIR

Session 7

Genome browsers- EnSembl, VEGA, VISTA, UCSE genome

Session 8

Database search engines- Entrez, DBGET

Session 9

File formats- GenBank, Fasta, ALN/ClustalW2

Session 10

Similarity based search engines-BLAST & FASTA

Session 11

Practice-1: Data retrieval using GenBank, SRS and DBGET


Session 12

Practice-2: Sequence similarity using BLAST

Session 13


Session 14

Sequence similarity-Basic concepts

Session 15

Scoring matrices-PAM, BLOSUM

Session 16

Pairwise alignment-Basic concepts, gap penalties

Session 17

Pairwise algorithm-Needleman & Wunsch, Smith & Waterman

Session 18

Pairwise alignment in nucleic acids and proteins

Session 19

Multiple sequence alignment-Basic concepts

Session 20

MSA- Heirarchial & Progressive approaches


Session 21

MSA algorithm- ClustalW & HMM based

Session 22

Introduction to phylogenetic analysis

Session 23

Methods of phylogeny- Maximum likelihood, Neighbor joining, Maxmum parsimony

Session 24

Practice-3: MSA using Clustal omega

Session 25

Practice-4: Phylogenetic analysis using MEGA

Session 26


Session 27

Nucleic acid sequence analysis-Reading frames, Transcriptional & Translational signals prediction

Session 28

Splice site identification, Detection of intron-exons, Gene prediction methods

Session 29

RNA fold analysis using MFOLD

Session 30

Protein sequence analysis- Hydropathy plot, pI/Mw detection

Session 31

Transmembrane prediction, protein localization tools

Session 32

Secondary structure prediction tools

Session 33

Structural Bioinformatics in Drug Discovery

Session 34

Quantitative structure-activity relationship (QSAR) techniques in Drug Design

Session 35

Protein Homology modeling

Session 36

Protein Predicted modeling

Session 37

Practice-5: Molecular docking

Session 38

Practice-6: Gene prediction tools

Session 39


Our Main Teachers

Gagan Kumar Panigrahi

Assistant Professor, Department of Zoology

Dr Rukmini Mishra

Assistant Professor

Dr Rukmini Mishra is presently working as an Assistant Professor (Botany), School of Applied Science, Centurion University of Technology and Management. She has a PhD in Agricultural Biotechnology from ICAR-National Rice Research Institute, India. After PhD, she received the prestigious Young Scientist Award from the Dept. of Science & Technology, SERB, Govt. of India to […]

Dr. Ranjan Kumar Sahoo

Associate Professor, Department of Biotechnology