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Introduction to Bioinformatics [1]

Paper Code: 
BIF 122
13.00
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.

9.00
Unit II: 
File Formats in Bioinformatics

Genbank, EMBL, Swissprot/Uniprot, PDB, Clustal, MSF, GCG, FASTA etc.

14.00
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

13.00
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.

11.00
Unit V: 
Tools for DNA & Protein Sequence Analysis

EMBOSS, PHYLIP, Mega2, CLustalX/W etc. Tools at NCBI, EBI, DDBJ, ExPasy

ESSENTIAL READINGS: 

1. Claverie and Notredame. “Bioinformatics - A Beginners Guide”. Wiley-Dreamtech India Pvt Ltd, 2003. 2. T.K Attwood & D.J Parry-Smith. Delhi. “Introduction to Bioinformatics”. Pearson Education (Singapore) Pte.Ltd., 2001. 3. 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. 4. David W. Mount. “Bioinformatics: Sequence and Genome Analysis” , New York, Cold Spring Harbor Laboratory Press, 2004.

REFERENCES: 

1. Dan E Krane, Elaine Nicpon Marieb, Michaeel L Raymer. “Fundamental Concepts of Bioinformatics”. Indian Edition, Benjamin Cummings Publication 2. David W Mount. “Bioinformatics: Sequence and Genome Analysis” Indian Edition. Cold Spring Harbour Laboratory Press. 2004. 3. Arthur M Lesk. “Introduction to Bioinformatics”. Oxford University Press 4. Dan E. Krane and Michael L. Raymer. “Fundamental concepts of Bioinformatics” Low Priced Edition, Pearson Education. 5. A.D Davison, D.B. Page & G.A. Petsko “Current Protocols in Bioinformatics” by Baxevanis, New York, John Wiley & Sons Inc., 2004.

Academic Year: 
2018-2019 [2]

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[1] https://www.biotech.iisuniv.ac.in/courses/PG-Courses/Bioinformatics/Introduction-to-Bioinformatics
[2] https://www.biotech.iisuniv.ac.in/academic-year/2018-2019