Introduction to Bioinformatics

Paper Code: 
MBL 325 B
Credits: 
5
Contact Hours: 
75
Objective: 

Course Objectives:

This course will enable the students to –

  1. To understand what is computational Biology.
  2. To find a best matcfor a given DNA or protein sequence from the target databases
  3. Gain knowledge of various Biological databases and tools
  4. Make them aware the application of various computational tools in Bioinformatics and related subjects.

Course Outcomes (COs):

Course

Learning outcome (at course level)

Learning and teaching strategies

Assessment Strategies

Paper Code

Paper Title

 

MBL 325 B

 

Introduction to Bioinformatics

 

Upon completion of the course students will be able to

CO 74 B: To get introduced to the basic concepts of Bioinformatics and its significance in Biological data analysis

CO 75 B: Overview about types and Biological data and database search tools

CO 76 B: Explain about the methods to characterise and manage the different types of Biological data.

 CO 77 B: Classify different types of Biological Databases

CO 78 B: Explain about the concept of pairwise sequence alignment , algorithms and tools for pairwise alignment method

 

  Approach in teaching:

Interactive Lectures, Discussion, Tutorials, Reading assignments, Demonstration, Team teaching

Learning activities for the students:

Self learning assignments, Effective questions, Giving tasks

Class test, Semester end examinations, Quiz, Solving problems in tutorials, Assignments, Presentation
 

 

 

 

16.00
Unit I: 
Introduction
  • Definition, History and Application areas of Bioinformatics.
  • Major Information Resources: NCBI, EBI, ExPasy, TIGR, JGI, DDBJ
  • Biological Databases: Primary & Secondary; Structure Databases, Specialized Databases, Chemical Databases, Entrez and SRS, Sequin & Bankit.
12.00
Unit II: 
File Formats in Bioinformatics
  • Genbank
  • EMBL
  • Swissprot/Uniprot
  •  PDB
  • Clustal
  • MSF
  • GCG
  • FASTA etc.
17.00
Unit III: 
Sequence Similarity Searching

·         Basics of sequence alignment

·         Local and Global Sequence Alignment

·         Similarity, Identity, homology

·         Sensitivity/Selectivity,

·         Scoring System & Substitution Matrices: Distance and Similarity matrices

Identity Matrices, PAM & BLOSUM matrices & their Derivation

16.00
Unit IV: 
Similarity Searching Tools
  • BLAST and FASTA, Theory and Algorithms, variants of BLAST and FASTA,
  • PSI & PHI Blast, Statistical Significance.
  • Sequence Pattern and Profiles: Concepts of motif, pattern and profile.
  • Profile construction and its application in Bioinformatics.
14.00
Unit V: 
Tools for DNA & Protein Sequence Analysis
  • EMBOSS,
  • PHYLIP,
  • Mega2,
  • CLustalX/W etc.
  • Tools at NCBI, EBI, DDBJ
  •  ExPasy
ESSENTIAL READINGS: 

BOOKS RECOMMENDED:

  • Claverie and Notredame. “Bioinformatics - A Beginners Guide”. Wiley-Dreamtech India Pvt Ltd, 2003.
  • T.K Attwood & D.J Parry-Smith. Delhi. “Introduction to Bioinformatics”. Pearson Education (Singapore) Pte.Ltd., 2001.
  • A.D Baxevanis & Ouellettee, B., F. F. “Bioinformatics: A Practical Guide to the analysis of Genes and Proteins” 2nd Edition, John Wiley & Sons, Inc. Publications, New York, 2002.
  • David W. Mount. “Bioinformatics: Sequence and Genome Analysis” , New York, Cold Spring Harbor Laboratory Press, 2004.
Academic Year: 
2021-2022
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