Syllabus
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Course Code: BOT-404 Course Name: e) Genomics (elective) |
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| MODULE NO / UNIT | COURSE SYLLABUS CONTENTS OF MODULE | NOTES |
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| 1 | 1. Genome: Completely sequenced prokaryotic (T4, and λ phages; E. coli) and eukaryotic genomes (Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Oryza sativa, Mus musculus and Homo sapiens); Mitochondrial and Chloroplast genomes. 2. Mapping of Genome: Genetic mapping- using DNA markers and Linkage analysis; Physical mapping- restriction mapping, Fluorescent in-situ hybridization and Sequence Tagged Sites (STSs) mapping. |
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| 2 | 3. Genome sequencing: Chain termination and chemical degradation methods; Next generation sequencing (NGS)- Pyrosequencing, SOLiD sequencing, Bridge amplification sequencing, Assembly of a contiguous DNA sequence- shotgun and clone contig methods, Human Genome Project. 4. Understanding a Genome Sequence: Gene location using 1.) ORF scanning, Automatic annotation, Homology searches and comparative genomics. 2.) Experimental techniques- northern hybridization, cDNA sequencing and RACE. |
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| 3 | 5. Identification of a Gene Function: Using computer analysis; Experimental analysis- gene inactivation and overexpression; Directed mutagenePsis; Reporter genes and Immunocytochemistry. 6. Analysis of the Transcriptome: Expressed Sequence Tags (ESTs); Serial analysis of gene expression (SAGE); Differential Display (DD); Representational Difference Analysis (RDA) and DNA Microarrays. 7. Proteome Analysis: Using 2-D; Protein identification; Protein-DNA and Protein- Protein interactions and Biochips. |
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| 4 | 8. Biological Databases: Introduction; Primary and Specialized Databases; Database Scheme; Database Annotation; Retrieval System; Nucleotide Databases; Protein Databases; Genomic Databases and Resources; Gene Databases and Resources; Transcriptome Databases; Mutation Databases; Mitochondrial Databases and Resources. 9. Computational Methods for Analysis of Genome Sequence Data: Introduction; Dot-Plot Matrix; Sequence pairwise alignment; Database searching; Multiple alignment; Alignment profiles to recognize distantly related protein or protein modules; Methods for sequence assembly; Linguistic analysis of biosequences; Prediction of RNA secondary structures; Protein sequence analysis; Evolutionary and phylogenetic analysis. |
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