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GENOMICS & PROTEOMICS Subject description : This paper deals with genome map, comparative genomics, structural genomics, functional genomics, protein structure prediction and function and various tools for analysis of proteins. Goals: To make the students to familiar with genome map, comparative genomics, structural and functional genomics and Proteomics —extensively used in drug discovery, and in learning various tools for analysis of proteins Objectives: To understand the genome architecture and extracting information like gene function, gene regulation, protein evolution and targets for drug designing.

UNIT I

Annotation of the Genome  Various approaches in gene prediction ORF prediction, Gene prediction in prokaryotes, Gene prediction in eukaryotes, Pattern discrimination, Evaluation of gene prediction method, Prediction of promoter sequences.  Genome analysis Chromosome rearrangement, Compositional analysis, Clustering of genes, Composite genes.

UNIT I
I

Functional Genomics Gene expression analysis by cDNA micro arrays, SAGE, Strategies for generating ESTs and full length inserts; EST clustering and assembly; EST databases (DBEST, UNIGENE); Expression and regulation of entire set of genes, Sporulation Vs Vegetative condition in yeast and Bacillus.

UNIT I
II

Comparative Genomics  Purpose and Methods of comparison Methods of comparison, Comparison at Nucleotide level, Breakpoints level, Gene cluster level.  Applications of comparative Genomics Predicting function, Predicting regulatory elements, Analysis of conserved strings.

UNIT-IV  Principles of Protein classification: Based on Structural features, Phylogenetic relationship, CATH - Classification by Class, Architecture, Topology, Homology, SCOP - Structural Classification Of Protein, FSSP - Fold classification based on structure - structure alignment, MMDB - Molecular Modeling Database, SARF - Spatial arrangement of backbone fragments

UNIT - V Proteome analysis  2D Electrophoresis Immobilized pH gradient, Sample preparation, First dimension criteria, second dimension criteria, Stabilization, Detecting protein on gel, Electro blot, Image analysis, Digital imaging, Spot detection and quantification, Gel matching

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