Syllabus
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Course Code: MMB-304 Course Name: Basics of Bioinformatics |
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| MODULE NO / UNIT | COURSE SYLLABUS CONTENTS OF MODULE | NOTES |
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| 1 | Introduction, overview and needs of bioinformatics technology. Biological databases – nucleic acid, genome, protein sequence and structure, gene expression databases, Database of
metabolic pathways, SNP, chemical, metabolic pathways, signalling pathways, general human genetics, cancer gene. Mode of data storage - File formats - FASTA, Genbank and Uniprot, Data submission & retrieval from NCBI, EMBL, DDBJ, Uniprot, PDB. |
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| 2 | Introduction to sequence alignment and its applications. Pair wise sequence alignment: Concept of global and local alignment, Dot Plot, algorithm for pair wise sequence alignment (Needleman Wunsch, Smith-watterman methods). Introduction to BLAST: types of BLAST, algorithm of BLAST and interpretation of its result. Substitution matrices: Introduction to substitution matrices: PAM and BLOSUM matrices, concept of log odd ratio. |
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| 3 | Multiple sequence alignment: Methods of multiple sequence alignment, Tools of MSA–
ClustalW, TCoffee; Position specific scoring matrices, introduction to consensus sequences, motifs and profiles. Significance of alignments: E value, Scores Diversity of Genomes: Viral, prokaryotic & eukaryotic genomes. Basic concepts of Genome, transcriptome, proteome. |
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| 4 | Phylogenetic Analysis: Introduction to phylogenetic analysis and its application. Types of
phylogenetic trees, Different approaches of phylogenetic tree construction - UPGMA,
Neighbour joining, Maximum Parsomony, Maximum likelihood. Genome Annotation: Concept of genome annotation, methods of gene identification. Tools of gene identification: GenScan, Grail, GeneID and Glimmer. Suggested readings: 1. Baxevanis AD, Ouellette BFF. Bioinformatics: A practical guide to the analysis of genes and proteins (John Wiley and Sons). 2. Rastogi S.C., Mendiratta N. and Rastogi P. Bioinformatics: methods and applications, genomics, proteomics and drug discovery, 2nd ed. Prentice Hall India Publication 3. Lesk M.A. Introduction to Bioinformatics. Oxford Publication, 3rd International Student Edition 4. Primrose and Twyman. Principles of Genome Analysis & Genomics. Blackwell 5. Attwood TK & Parry-Smith DJ. Introduction to Bioinformatics. Pearson Edu. |
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