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BIF303 Genomics and Proteomics LTPC: 3 0 2 4

Version No. 1.1.0Course Prerequisites Biochemistry, Cell Biology and Genetics

Objectives: To equip the students with the basics and applications of genomics and proteomics.

Expected Outcome: To realize the importance of genomic and proteomic studies2. To understand the techniques involved in the analysis ofgenomics and proteomics3. To utilize the genomic and proteomic patterns in industrialand medicinal diagnostics and treatment

Unit No. 1 Gene structure and sequencing Number of hours: 9

Sequence complexity introns and exons genome structure in viruses andprokaryotes organelle genomes and nuclear DNA in eukaryotes chain terminatorsequencing automated DNA sequencing high throughput sequencing alternateDNA sequencing methods.

Unit No. 2 Comparative genomics and Globalexpression profiling

Number of hours: 9

Protein evolution by exon shuffling comparative genomics of prokaryotes andeukaryotes horizontal and lateral gene transfer Traditional approaches toexpression profiling- global analysis of RNA expression: spotted DNA arrays, printedoligonucleotide chips data acquisition and analysis serial analysis of geneexpression massively parallel signature sequencing.Unit No. 3 Functional and structural

genomicsNumber of hours: 9

Functional genomics by systematic gene knockout genome wide randommutagenesis use of chemical mutagens and phenocopy libraries Determininggene function by sequence comparison X-ray crystallography and NMR in highthroughput structure determination structure prediction methods domain fusionmethod for functional annotation.

Unit No. 4 Proteome mining and Proteinsequencing

Number of hours: 8

Gel electrophoresis (1DE and 2DE), liquid chromatography and mass spectrometersfor protein and peptide analysis routes in proteome analysis - protein digestiontechniques - protein identification by mass finger printing sequence analysis bytandem mass spectrometry data bases and algorithms in protein identificationUnit No. 5 Protein Expression analysis,

interaction network andmodifications

Number of hours: 10

Comparative proteomics use of isotope tags yeast two hybrid systems immunoprecipitation and western blot analysis short gun identification ofmultiprotein complex bait and reverse bait analysis protein-protein and protein-DNA interactions protein interaction network sample enrichment for detectingprotein modifications integration of different algorithms to map proteinmodification- glycoprotein analysis protein arrays.

Text Books 1. Principles of genome analysis and genomics SB Primrose and RMTwyman, 3rd edition, Blackwell publishing, 2003.

2. Introduction to proteomics: tools for the new biology Daniel CLiebler, Humana Press, 2002.

References Discovering genomics, proteomics and bioinformatics, A MalcolmCampbell and Laurie J Heyer, Cold Spring Harbour Laboratory Press,2002.

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Mode ofEvaluation

Announced / Unannounced Quiz / tests, Assignments and WrittenExaminationList of Experiments

1. Proteomics [Aldente (PMF), Popitam (MS/MS), Phenyx (MS/MS),FindMod, PeptideMass, .]2. DNA -> Protein [Translate]

3.Similarity searches [BLAST]4. Pattern and profile searches [ScanProsite]5. Post-translational modification and topology prediction6. Primary structure analysis [ProtParam, pI/MW, ProtScale]7. Secondary and tertiary structure prediction [SWISS-MODEL, Swiss-PdbViewer]8. Alignment [Nomad, T-COFFEE, SIM]9. Phylogenetic analysis10. Biological text analysis11. 2D gel database analysis

Recommended by the Board of Studieson 11th November 2009

Approved by 19th Academic Council

http://phenyx.vital-it.ch/pwi/?xtor=25http://www.expasy.org/tools/#similarityhttp://www.expasy.org/tools/#similarityhttp://www.expasy.org/tools/#similarityhttp://phenyx.vital-it.ch/pwi/?xtor=25