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in Biotechnology (2024 Admitted Batch)
COMPUTATIONAL BIOLOGY
Course Code: BT30005
Credit: 3
L-T-P: 2-0-2
Prerequisite: Nil
Course Description:
In this course, students will understand the fundamentals of the development and application
of computational methods such as data analysis, mathematical modeling, and simulation to
analyze large collections of biological data, such as genetic sequences, cell populations, or
protein samples, to make new predictions or discover new biology. This course includes the
different databases of biological information, such as sequences and structures of DNA, RNA,
and protein, and computational studies on genome assembly, gene prediction, and system
biology.
Course Outcomes:
At the end of the course, the students will be able to:
CO1: Learn the basic concepts, overview, and application of bioinformatics.
CO2: Understand different biological databases, including the sequences and structures of
DNA, RNA, and protein.
CO3: Analyze the sequence alignment, genome sequencing, gene prediction methods,
phylogenetic tree construction, and protein secondary structure prediction methods.
CO4: Evaluate the use of bioinformatics in application-oriented studies such as computer-
aided drug design and systems biology.
CO5: Design and integrate the knowledge of bioinformatics and systems biology in
understanding advanced courses like genomics and proteomics.
CO6: Acquire a comprehensive understanding of the essential aspects of bioinformatics and
develop professional skills to apply the knowledge in the related fields both in
academia and industry.
Course Contents:
Unit-1: Biological Databases: Sequence databases: Nucleotide and protein databases; Gene
expression databases, 3D-structure databases, pattern and motif databases.
Unit-2: Sequence Alignment and Homology: Pair-wise sequence alignment, Concepts,
alignment scores, substitution matrices; Dot Plots and Algorithms: Needleman-Wunsch
(global alignment) and Smith-Waterman (local alignment); Homology and Similarity:
orthologs, paralogs; Database Searching: BLAST and its variants, interpretation of hits and
statistical significance; Multiple Sequence Alignment (MSA): Importance, scoring schemes,
progressive and iterative algorithms; Domain search: Position-specific scoring matrix;
Applications of MSA: Phylogenetic tree construction, taxonomy, comparative genomics.
Unit-3: Genome Analysis and Phylogenetics: Genome Assembly Approaches: De novo
assembly: de Bruijn graph-based methods, Reference-based assembly: Alignment to known
genomes. Gene Prediction: Prokaryotic and eukaryotic gene prediction, Expression-based
methods (RNA-Seq, ESTs) and de novo prediction algorithms; Functional Enrichment
Analysis; Phylogenetic analysis: distance-based and character-based methods.
Unit-4: Structure Prediction and Drug Design: Secondary structure prediction, signal
peptide prediction. Tertiary structure prediction: Homology modeling, Structure-based drug
design: Scoring functions and molecular docking.
Unit-5: Systems Biology and Network Analysis: Biological Networks: Protein-protein
interaction (PPI) networks, Protein-DNA and gene regulatory networks; Network
Visualization and Analysis.
Textbook:
1. Bioinformatics: Sequence and Genome Analysis, Second edition. Authors: David M.
CSHL Press, 2004.
Reference books:
1. Introduction to bioinformatics, Fifth edition. Author: Lesk A. Oxford University Press,
2019.
2. Bioinformatics: A practical guide to the analysis of genes and proteins, Third edition.
Authors: Baxevanis AD, Ouellette BFF. Wiley-Interscience, 2004.