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INTRODUCTION TO BIOINFORMATICS [1]

Paper Code: 
MBL 325 B
Credits: 
05
Contact Hours: 
75
Objective: 

Course Outcomes (COs):

 

Learning outcome (at course level)

Learning and teaching strategies

Assessment Strategies

Upon completion of the course the learner will

CO 96 B: To get introduced to the basic concepts of Bioinformatics and its significance in Biological data analysis

CO 97 B: Overview about types and Biological data and database search tools

CO 98 B: Explain about the concept of pairwise sequence alignment, algorithms and tools for pairwise alignment method

CO 99 B: Learn similarity searching tools

CO 100 B: Learn tools for DNA anf protein sequence analysis.

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

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: 
  • BIOINFORMATICS SEQUENCE AND GENOME ANALYSIS 2ED Publisher CBA 2005
  • Knowledge-Based Bioinformatics: From Analysis to Interpretation. Gil Alterovitz (Editor), Marco Ramoni (Editor). Publisher Wiley 2010.
  • David W. Mount. “Bioinformatics: Sequence and Genome Analysis” , New York, Cold Spring Harbor Laboratory Press, 2004
REFERENCES: 

SUGGESTED READINGS:

  • 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.
  • Bioinformatics and Data Analysis in Microbiology. Bishop Ozlem Tastan (Author). Caister Academic Press. 2014

e RESOURCES:

JOURNALS:

  • Advances in Bioinformatics
  • Research Journal of Life Sciences, Bioinformatics, Pharmaceutical and Chemical Sciences
  • Current Bioinformatics
Academic Year: 
2022-2023 [5]

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Source URL: https://www.biotech.iisuniv.ac.in/courses/subjects/introduction-bioinformatics-6

Links:
[1] https://www.biotech.iisuniv.ac.in/courses/subjects/introduction-bioinformatics-6
[2] https://www.ncbi.nlm.nih.gov/
[3] https://www.ncbi.nlm.nih.gov/guide/data-software/
[4] https://www.ddbj.nig.ac.jp/index-e.html
[5] https://www.biotech.iisuniv.ac.in/academic-year/2022-2023