INTRODUCTION:
Introduction to Genomics & Proteomics. Structure, Organization and features of Prokaryotic & Eukaryotic genomes. C-values of eukaryotic genomes - coding, noncoding and repetitive sequences. Organisation of genome within nucleus, mitochondria and chloroplast. Genome mapping: Genetic and physical mapping. Polymorphisms. Molecular markers – RFLP, AFLP, RAPD, SCAR, SNP, ISSR, and Protein markers – Allozymes and Isozymes, Telomerase. FISH – DNA amplification markers and Cancer biomarkers.
GENOME SEQUENCES DATABASES AND GENOME ANNOTATION:
Extrinsic, Intrinsic (Signals and Content), Conservative information used in gene prediction. Frameworks for Information integration – Exon chaining. Generative models: Hidden MorkovModels,Discriminative learning and Combiners. Evaluation of Gene prediction methods – Basic tools, Systematic evaluation and Community experiments (GASP, EGASP and NGASP). and Gene Ontology.Functional annotation of Proteins: Introduction, Protein sequence databases, UniProt
UniProtKB :
Sequence curation, Sequence annotation, Functional annotation, annotation of protein structure, post-translational modification, protein-protein interactions and pathways, annotation of human sequences and diseases in UniProt and UniProtKB. Protein family classification for functional annotation – Protein signature methods and Databases, InterPro,InterProScan for sequence classification and functional annotation. Annotation from Genes and Protein to Genome and Proteome
GENOME SEQUENCING:
Recent developments and next generation sequencing, ultrahighthroughput DNA Sequencing using Microarray technology. Genome sequencing projects on H. Influenzae, E. coli, OrizasativumandNeem. Human-genome project. Raw genome sequence data, Gene variation and associated diseases, diagnostic genes and drug targets. Genotyping-DNA Chips. Comparative and Functional Genomics: Studies with model systems such as Yeast, Drosophila, C. elegans, Arabidopsis. Approaches to analyze global gene expression – transcriptome, Serial Analysis of Gene Expression (SAGE), Expressed Sequence Tags (ESTs), Massively Parallel Signature Sequencing (MPSS), microarray and its applications, gene tagging
Proteomics:
Scope, Experimental methods for studying proteomics, methods of protein isolation, purification and quantification. Methods for large scale synthesis of proteins.Applications of peptides in biology. Analysis of proteome – High throughput screening – Yeast two hybrid system and Protein chips, engineering novel proteins, Mass Spectroscopy based protein expression and posttranslational modification analysis. Bioinformatics analysis – clustering methods. Analysis of proteome functional information.