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Introduction to Bioinformatics
OBJECTIVE:
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To get introduced to the basic concepts of Bioinformatics and its significance in Biological data analysis. |
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Overview about types and Biological data and database search tools. |
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Explain about the methods to characterise and manage the different types of Biological data. |
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Classify different types of Biological Databases. |
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Explain about the concept of pairwise sequence alignment , algorithms and tools for pairwise alignment |
Course Outcomes (COs):
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Course |
Learning outcome (at course level) |
Learning and teaching strategies |
Assessment Strategies |
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Paper Code |
Paper Title |
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MBL 325 B
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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 alignmentmethods of taxonomy . |
Approach in teaching: Interactive Lectures, Discussion, Tutorials, Reading assignments, Demonstration, Team teaching
Learning activities for the students: Self-learning assignments, Effective questions, Seminar presentation, Giving tasks
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Class test, Semester end examinations, Quiz, Solving problems in tutorials, Assignments, Presentation |
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.
Genbank, EMBL, Swissprot/Uniprot, PDB, Clustal, MSF, GCG, FASTA etc.
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
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.
EMBOSS, PHYLIP, Mega2, CLustalX/W etc. Tools at NCBI, EBI, DDBJ, ExPasy
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.
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.
