VINAYAKA MISSIONS UNIVERSITY AARUPADAI VEEDU INSTITUTE OF TECHNOLOGY, PAIYANOOR & VMKV COLLEGE OF ENGINEERING, SALEM DEPARTMENT OF BIOINFORMATICS

QUESTION BANK SUBJECT: PROTEOMICS CLASS/ SEMESTER: III / V REGULATION: 2006 UNIT I: Introduction to Proteomics & Proteome PART-A 1. Define Proteome. 2. What is proteomics? 3. Define Database. 4. Differentiate Proteomics from genomics. 5. Write the role of Ubiquitin. 6. List out the tools used in protein study. 7. How can you degrade proteins? 8. What is codon bias? 9. Define protein. 10. What is gene expression? 11. How can you deduce a protein? 12. List out the methods used to evaluate a protein 13. Give a list of protein Databanks 14. What do you mean by death of protein? 15. Define genome PART-B 1. Explain in detail how will you evaluate a protein? 2. Discuss in detail about life and death of proteins. 3. Give detailed account on degradation of protein. 4. Explain in detail about Gene expression. 5. Discuss proteins as modular structure. 6. Explain how will you deduce proteome from genome? 7. Explain about ubiquitination 8. How can you degrade a protein? Explain. 9. List out the detailed applications of proteomics 10. Give a schematic presentation for life cycle of protein UNIT- II Protein Engineering & Folding PART-A 1. List out the bonds involved in protein folding. 2. Define genetic code. 3. Give short notes on quaternary structure of proteins.

4. What do you mean by proteins folding patterns? 5. Define modular proteins. 6. Give short notes on Protein turn over. 7. What is domain swapping? 8. Define Chevron plot. 9. Write short notes on folding funnels. 10. What do you mean by protein folding? 11. Give short notes on the effect of denaturants. 12. What is the thermodynamics of protein folding? 13. Define native form of protein 14. What are chaperones? 15. Define domains. PART-B 1. Explain about the effect of denaturants on the rate of proteins folding. 2. Explain about Molten globule in detail. 3. What do you mean by protein turnover? Explain. 4. Discuss about the thermodynamics of protein folding. 5. Explain the process involved in protein folding. 6. Give a detailed note on folding and unfolding Chevron plots. 7. Give a detailed description on control of protein function 8. Explain protein folding patterns in detail. 9. What happens if protein is misfolded? Discuss. 10. Give detailed note on Thermodynamics of protein.

UNIT III Protein structure Prediction & Design PART-A 1. Define CSAP. 2. What is threading? 3. Give short notes on Protein designing. 4. What is the role of Chaperones? 5. Define homology modeling. 6. Differentiate homology modeling and Threading. 7. How can you predict novel folds? 8. Give short notes on phylogenetic trees. 9. What is the role of Tumor supressor genes? 10. List out the features of secondary structure of protein 11. What do you mean by multiple motif? 12. List out the steps involved in designing a protein 13. List out the steps involved in predicting protein structure 14. What do you mean by novel folds? 15. List out the programs used in protein structure prediction PART-B

1.Discuss about the prediction of protein structure. 2.Give a detailed account on prediction of protein function. 3.Explain about protein designing in detail. 4.Discuss about conformational energy calculation and molecular dynamics. 5.Explain why protein exists as Protein-protein partner. 6.Discuss on prediction of novel folds 7. Define CSAP and explain it. 8.Discuss about various programs used in protein study. 9.Explain in detail about homologus proteins. 10. Write about Rosetta and Linus program in detail. UNIT- IV Tools for Proteomics PART-A 1. Give the principle of MS 2. What is the significance of SDS PAGE? 3. How can you ionize sample in MS? 4. What is the use of antibodies in Proteomic study? 5. Define MALDI _ TOF. 6. How can you digest the proteins? 7. Expand ICAT. 8. Differentiate MALDI _ TOF from ESI. 9. What is peptide mass finger printing? 10. What are the problems with 2D SDS-PAGE? 11. Write the pros and cons of MALDI 12. Expand SALSA 13. Give the role of trypsin 14. Differentiate MALDI and ESI 15. Give the applications of SALSA PART-B 1. How is proteins identified by peptide mass fingerprinting? Explain 2. Discuss about protein Digestion Techniques. 3. Explain about the different types of analyzers used in protein determination. 4. How will you determine the mass of a protein? Explain 5. What is ESI? Explain in detail. 6. Explain the tools involved in protein study. 7. Give a detailed note on peptide sequence analysis. 8. Explain about peptide ion fragmentation 9. What is SALSA and list out its applications 10. Explain in detail about MALDI-TOF UNIT V Applications of Proteomics PART-A 1. Define mining. 2. Expand MALDI - TOF.

3. List out the merits of MALDI TOF. 4. What are protein arrays? 5. List out the types of analyzers. 6. What do you mean by mapping of protein? 7. Write short notes on robotic automation. 8. What do you mean by protein- protein interaction? 9. Give schematic presentation for supershift. 10. How can you integrate Sequest and SALSA to map protein modifications? 11. What is protein network mapping? 12. How can you select proteome for analysis? 13. Why are antibodies used in protein study? 14. Give the significance of 2D-SDS PAGE 15. What are analysers? PART-B 1. Discuss about the applications of proteomics. 2. Explain the new Direction in proteomics. 3. What do you mean by mining? Explain in detail. 4. How can you profile the protein expression? Explain 5. What are techniques used to determine protein protein interactions? Explain 6. How is SALSA used in Map protein modification? Explain 7. Give a detailed explanation on immunoprecipitations. 8. Explain about multidimensional peptide chromatography and LC-Tandem MS Analysis 9. Discuss on deducing modifications from MS Data 10. Explain the new directions in proteomics

VINAYAKA MISSIONS UNIVERSITY AARUPADAI VEEDU INSTITUTE OF TECHNOLOGY, PAIYANOOR & VMKV COLLEGE OF ENGINEERING, SALEM DEPARTMENT OF BIOINFORMATICS QUESTION BANK SUBJECT: BIOPHYSICS YEAR/SEM: III/V REGULATION: 2006 Unit 1 - Classical Mechanics PART-A 1. Define a quantum. 2. Write Schrdinger wave equation. 3. List the differences between configuration and conformation of a biomolecule. 4. What does uncertainty principle states? 5. Differentiate a molecular orbital and an atomic orbital. 6. Write short notes on the structure of an atom. 7. Give short notes on -pleated sheets 8. How are the different conformations of proteins depicted on ramachandran plot? 9. What are atomic fluctuations? 10. What are phi and psi angles? Give their significance. 11. What do you mean by C ? 12. What is an orbital? 13. Differentiate classical and quantum mechanics. 14. Give the physical significance of wave function. 15. State the principle of virtual work. 16. What do you understand by term Mechanics? 17. What is D Alemberts principle? 18. What is the central paradigm of biophysics? 19. Write an expression for De Broglies wavelength and explain the terms involved in it. 20. Write short notes on Plancks quantum theory. PART-B 1. What are the different principles of quantum mechanics? Explain 2. Explain the macromolecular structures of proteins & techniques used to elucidate the dynamics at atomic level. 3. Explain the secondary structure of protein molecules in detail. 4. Explain the different conformations in protein molecule. 5. Explain the different types of weak interactions in a biomolecule. 6. Starting from principle of virtual work, derive an expression for Lagranges equation. 7. Derive Hamiltons canonical equations of motion. 8. Derive Schredingers time independent wave equation. 9. Explain uncertainty principle. Give an experimental evidence to prove this principle. 10. Describe the chemical structure of nucleic acids.

Unit 2 - Bioenergetics Principles PART-A 1. Define Entropy. 2. What are the hydrophobic effects? 3. Define equilibrium constant and explain with an example. 4. What are exergonic and endergonic reactions? 5. Define molecular dynamics simulation. 6. Write short notes on the additive nature of free energy. 7. Define system. Give different types. 8. Write short notes on the structure of ATP. 9. Define Enthalpy. 10. Give brief account on the concept of energy. 11. Define the standard free energy of formation for a biochemical reaction. 12. What do you mean by simulation? 13. Differentiate intensive and extensive properties. 14. State first law of thermodynamics. Give its limitation. 15. State Le Chateliers principle. 16. What are the standard conventions in bioenergetics? 17. What do you understand by term Thermodynamics? 18. Write short notes on spontaneity of a reaction. PART-B 1. 2. 3. 4. 5. 6. 7. 8. Explain the different criteria for a reaction to be spontaneous. Explain the energy minimization involved in simulating a macromolecular structure. Describe in detail about molecular dynamics. Explain the laws of thermodynamics in detail. Write detailed account on enthalpy and entropy. ATP is the universal currency of free energy in biological systems. Discuss in detail. Explain the free energy methods in molecular simulation. Discuss in detail the importance of bioenergetics in bioinformatics. 9. Consider reversible reaction, DHAP G 3 P. At equilibrium, the equilibrium constant at 298 K is 0.0475. The initial concentrations of DHAP and G 3 P are 2 x 10-4 M and 3 x 10-6 M respectively. Determine whether the reaction is endergonic or exergonic. Unit 3 - Kinetics of Biological systems PART-A 1. 2. 3. 4. 5. What is active transport? Give the composition of plasma membrane in eukaryotic cells What are the different types of transport mechanisms across the cell membrane? Who proposed the fluid mosaic model of cell membrane structure? What is endocytosis?

6. What is pinocytosis 7. Give short notes on sodium potassium ion pump. 8. Write in brief about ATP hydrolysis. 9. What are the different types of proteins present in the cell membrane? 10. How do membrane carbohydrates contribute to cell signaling? 11. Give short notes on passive diffusion 12. What is the role of peripheral proteins in cell transport? 13. What is the role played by pore in cell transport ? 14. Write short notes on Uniport 15. Give short notes on facilitated transport process, PART-B 1. 2. 3. 4. 5. 6. Explain the nerve impulse using neurotransmitters. How is transport across the cell membrane controlled? Explain Explain in detail the structure and components of a cell membrane. Give different models proposed for the structure of the cell membrane. Explain Explain the different types of Transport mechanisms across the cell membrane. Elucidate the possible profiles of facilitated transport of molecules or ions across the cell membrane. 7. Write in detail about the ion pump with its significance 8. Give the composition of plasma membrane in detail. Unit 4 - Kinetics of biomolecular interactions PART-A 1. 2. 3. 4. 5. 6. Write short notes on the bond angles phi and psi for a given biomolecule. Give an account on Resonance What are van der Waals radii? Define Michaelis Mentan constant. What is kinetic rate constant? What are a) heterotrophic interactions b) homotrophic interactions 9. Name some folding accessory proteins. 10. Differentiate conformation and configuration. 11. Write short notes on the rate of reaction. 12. What is the principle of NMR spectroscopy? 13. Define catalytic efficiency. 14. Write short notes on the steady state kinetics. 15. How will you calculate the kinetic rate constant? 18. Give short notes on protein folding.

PART-B

1. 2. 3. 4. 5. 6.

Explain the resolution of protein structure in solution. Explain Ramachandran plot in detail. How does variation in substrate concentration effect biochemical kinetics? Explain Explain steady state kinetics with respect to a biochemical example. Describe protein folding along with their kinetics. Give different experiments in detail for the detection of intermediates in a biochemical reaction. 7. Explain protein ligand interaction with examples. Unit 5 - X-Ray Crystallography PART-A : 1. Define Braggs law. 2. What do you mean by diffraction? 3. Give short note on the structure of crystals. 4. Define a fiber unit cell 5. What are continuous helices? 6. What is Von laue condition for diffraction? 7. Give a brief note on fibre diffraction. 8. Describe discontinuous helices with examples. 9. Give short note on X-ray 10. What is the application of Coolidges tube? 11. Give short notes on Crystal morphology. 12. What do you mean by angle of rotation in fiber unit cell 13. Give short notes Meridinial reflections 14. What are Equatorial reflections? 15. What are Layered lines? 16. Write short notes on Z-axis in a fiber unit cell. 17. Give short notes Soft X-rays 18. What are hard X-rays? 19. What is photoelectric effect? 20. What do you mean by Laue pattern? 21. What is Vapor Diffusion? 22. Give short notes Macroseeding 23. Give the application of free interface diffusion. 24. What is batch crystallization? 25. Give short notes mounting the crystal. PART-B 1. Explain the different methods of growing crystals 2. How would you experimentally determine the crystal morphology? Explain 3. What are the conditions required for macromolecular crystallization? Explain

4. Explain in detail the principle, methodology and instrumentation of solving macromolecular structures by X ray crystallography. 5. Explain in detail the concept of fiber diffraction. 6. Elucidate the different methods of protein crystallization. 7. How the morphology of a crystal is determined using the principles of X-ray crystallography?

VINAYAKA MISSIONS UNIVERSITY AARUPADI VEEDU INSTITUTE OF TECHNOLOGY, PAIYANOOR. & VMKV ENGENEERING COLLEGE, SALEM. DEPARTMENT OF BIOINFORMATICS QUESTION BANK SUBJECT: COMPUTATIONAL BIOLOGY CLASS/ SEMESTER: III/V REGULATION: 2006 UNIT -1 Overview of computational biology PART-A 1. What is computational biology? 2. Define proteins 3. What are nucleic acids? 4. Give short notes on the applications of Computational Biology. 5. Define Sequence analysis. 6. What is sequence alignment? 7. List out the role of sequence analysis in Computational Biology. 8. Define motif. 9. What are the methods of motif finding? 10. Define energy field. 11. What do you mean by expression profiling? 12. List out the types of energy fields. 13. Define strings. 14. What is an algorithm? 15. Define Graphics. PART-B 1. Explain the role of proteins and nucleic acids in computational Biology. 2. Give a detailed note on the role of sequence analysis. 3. Discuss on Motif finding method in detail 4. Describe energy fields and its methods. 5. Give detailed notes on the Expression Profiling and its methods. 6. Explain the methods involved in quantitative Image analysis. 7. How does the expression profiling play an important role in a protein? Explain 8. Explain algorithms and their uses in computational biology. 9. Elucidate the quantitative image analysis. 10. Explain in detail about the analytical methods of protein and nucleic acids UNIT II: Sequence alignment: PART-A 1. Define heuristic approach. 2. List out the database search methods in sequence alignment. 3. What are the tools available in sequence alignment?

4. Define scoring matrices. 5. What is a gap penalty? 6. What do you mean by gap open penalty? 7. Define gap extension penalty. 8. State about PAM matrice. 9. Define BLOSUM matrice. 10. What is a distance matrix? 11. Define similarity matrix. 12. What are the values given to match, mismatch and gap? 13. List out some of the significances in a Sequence Alignment. 14. Define conservative substitution. 15. What do you mean by affine gap costs? 16. Define optimal alignment. PART-B 1. Elaborately answer the approaches available in finding sequence alignment. 2. Discuss about Scoring matrices and its methods. 3. Explain the database search methods and tools available in Sequence alignment. 4. Give a detailed note on PAM matrix. 5. Write detailed account on BLOSUM matrix. 6. Discuss on DOT matrix method. 7. Explain scoring matrices in detail. 8. Explain about distance matrix in detail. 9. Discuss the significances of sequence alignment in detail. 10. Elucidate the methods of Sequence alignment in detail. UNIT III: Multiple Sequence Alignment PART-A 1. What is Multiple Sequence Alignment? 2. Define pairwise sequence alignment 3. List out the applications of Multiple Sequence Alignment 4. What are the approaches of multiple sequence alignment? 5. Define Progressive method 6. What is Iterative method? 7. What do you mean by Profiles? 8. Define BLOCKS 9. Discuss the Patterns 10. What do you mean by Motifs? 11. Write about the conserved regions 12. Where do we use semi-conservative substitutions? 13. Define domain 14. Write short notes on Meme 15. Define Gibbs sampling method. 16. Write about Markov chain process 17. Define BLAST

PART-B 1. 2. 3. 4. 5. 6. 7. Explain the various approaches in MSA. Discuss the progressive and iterative methods. How does profile analysis play an important role in finding out MSA? Explain Explain in detail about BLOCK analysis. Give justification for the pattern searching and matching in detail Give detail about Motif finding analysis. Describe the statistical method of Expectation maximization algorithm for aiding sequence alignment in MSA. 8. How will you identify patterns by Gibbs sampler method? Discuss 9. Explain the states of Markov chain and discuss about its process. 10. List out the programs available in BLAST and FASTA and its accesing methods. UNIT IV: : RNASecondary structure and gene prediction PART-A 1. Define RNA. 2. How can we predict RNA secondary structure? 3. Define mfold. 4. What do you mean by RNA folding? 5. Define the structures of RNA folding. 6. What is RNA modeling? 7. Mention the programs available in modelling the RNA? 8. Define Gene prediction. 9. List out the methods for predicting the Gene. 10. Define neural networks. 11. List out the applications of neural network. 12. Define Pattern discriminations. 13. What do you mean by signal site? 14. Define splice site. 15. What do you mean by signal recognition? 16. Define promoter. 17. What do you mean by Fragment in DNA? PART B 1. Discuss RNA secondary structure prediction methods. 2. Justify the limitations of RNA structure prediction. 3. Explain in detail about motif folding. 4. List out the applications of RNA secondary structure modeling and explain how its used to predict the secondary and tertiary structure of RNA. 5. Explain some of the gene prediction methods available. 6. Discuss about the neural networks and its methods. 7. How the neural network applied in gene prediction method and its applications. 8. Discuss the evaluation methods in gene prediction. 9. Elucidate the various DNA computing methods. 10. Discuss about the fragment Assembly of DNA.

UNIT V: Genome Analysis PART-A 1. Write short notes on Genome. 2. Define Gene ontology. 3. What is Gene density? 4. Define Gene order 5. What do you mean by Gene synteny? 6. Define Gene plasticity zone. 7. Where do we use the Gene network? 8. Write short notes on Tandem repeats. 9. Write short notes on Clusters. 10. Write short notes on Pseudogene. 11. Define Non coding conversation. 12. What is Coding conversation? 13. Where do we find the Conservative region? 14. Define Functional genomics. 15. What is Structural genomics? 16. Write short notes on Comparative genomics. 17. Define Suffix tree. 18. What are the methods available in a Suffix Tree? 19. Define MUMMER. 20. Define MEGA BLAST PART-B 1. Give a detailed account on the approaches of suffix tree and its applications. 2. Explain in detail about the databases available for the analysis of a particular genome. 3. Discuss the methods used for predicting genome 4. Elaborate suffix tree analysis. 5. Explain about the transposable elements. 6. Discuss about the pseudogene and its methods. 7. Write the applications of pseudogene analysis in predicting a DNA in detail. 8. Explain gene clustering method 9. Elucidate BLAST in detailed manner 10. Describe FASTA in detail

VINAYAKA MISSIONS UNIVERSITY AARUPADI VEEDU INSTITUTE OF TECHNOLOGY, PAIYANOOR. & VMKV ENGINEERING COLLEGE, SALEM DEPARTMENT OF BIOINFORMATICS QUESTION BANK SUBJECT: GENOMICS CLASS/SEM: III/V REGULATION: 2006 UNIT 1 - Gene & Genomics PART-A 1. Define Gene. 2. Define Genomics. 3. Distinguish between Exons and Introns. 4. Draw the structure of prokaryotic genome. 5. Write the significance of ORF? 6. Define functional genomics. 7. What is cDNA? 8. Give the significant role of ddNTP 9. Define gene expression. 10. What is genome sequence annotation? 11. Define positive regulations. 12. Define negative regulations. 13. What is mutation? 14. What is allele? 15. What is structural genomics? 16. Name any three on-going projects relevant to genome annotation? 17. How different is one human genome from another? PART B 1. Explain in detail about Lac operon 2. What are the goals and applications of whole genome sequencing? Explain 3. Compare and discuss the principle and methodology of Capillary and slab gel electrophoresis 4. What are the traditional techniques to locate a gene? Explain 5. Enumerate the gene assembling tools in detail 6. Discuss in detail about genome variation. 7. Explain Sanger method with neat sketch. 8. How a eukaryotic gene is regulated? Explain in detail. 9. What is GMO? Explain with examples. 10. Give detailed notes on principle of genome annotation and list some annotation tools? UNIT 1I - Organization & function of Eukaryotic genomes

PART-A 1. Give the importance of Northern blot. 2. Give the importance of the southern blot technique. 3. Differentiate zoo blot and Northern blot. 4. What is a DNA chip? 5. Give the significance of cDNA library 6. Write short note on D loop. 7. What is Endosymbiotic theory? 8. Define a probe. 9. Write short notes on C value paradox 10. What are repeat sequences? 11. What is the role of tandomly repeated sequences 12. What is the significance of dispersed repeated sequences 13. What is a euchromatin? 14. Where a CpG island is found in the genome? 15. Write short notes on cy3 dye 16. Give the importance of cy5 dye. 17. Site out the reasons for high mutation rate in mtDNA. 18. Compare the genetic code of nuclear and mitochondrial genome. 19. What is a primer? 20. Draw the structure of cy3 and cy5 dyes. PART B 1. Enumerate the principle and methodology of micro array. 2. Enlighten the organization and function of chloroplast genome. 3. Enlighten the organization and function of mitochondrion genome. 4. What are the available methods for genome sequencing? Explain 5. Explore and assess the application of DNA chip technology in biological research. 6. Explain in detail about SAGE. 7. Explain the principle and factors affecting differential display analysis of gene expression 8. What are the different types of micro array? Explain with applications. 9. Explain subtractive DNA library screening by hybridization process. 10. Give detailed notes on principle and application of cDNA RDA techniques. UNIT III - Mapping & Sequencing of Genome 1. 2. 3. 4. 5. 6. 7. 8. PART-A What is the significance of STS? Define SNP. Give briefly the significance of ESTs. Define SSLP. What is RFLP? Write short notes on chromosome walking. What are Genome maps? Expand the term FISH.

9. Give the importance of cytogenetic maps 10. Give the advantages of HAPPY mapping 11. What are pseudogens? 12. Define low resolution physical maps. 13. Write notes on high resolution physical maps. 14. Write short notes on restriction enzymes. 15. Give the importance of the technique FISH 16. What is genetic crossover? 17. Write short notes on PCR 18. What is the significance of genetic map? 19. What is cDNA? 20. Write short notes on transposable elements. PART B 1. Clearly explain the differences between genetic and physical map of a genome. 2. Explain why are maps required for the sequencing of genomes? 3. Explain in detail about genetic linkage maps and its applications? 4. How does a scientist prepare a clone library from just a single chromosome? Explain 5. How are restriction enzymes used to generate both genetic and physical map? Discuss 6. What are the various types of physical maps? Explain. 7. Give detailed account on the techniques involved in generating a genetic map. 8. What are the techniques involved in cytogenetic mapping? Discuss 9. Explain the merits and demerits of high resolution and low resolution maps. 10. Enumerate the principle of STS maps.

UNIT IV Genome PART-A 1. Give the importance of PEDENT 2. Expand the term COG 3. Write short notes on the database KEGG 4. Give the advantages of WIT 5. Write short notes on MBGD 6. Give the significance of HGP. 7. What is the sequencing technique used in HGP? 8. Give the advantages of genome databases. 9. Give the applications of KEGG 10. Define computational genomics 11. Write the applications of computational genomics 12. Give any 5 important genes of Fungi along with its function. 13. Write notes on any 2 bacterial proteins whose structure is been elucidated? 14. What are the databases available to study bacterial genomes?

15. Give the links generally used to study the fungal genomes. 16. Give any 5 gene names along with their function of a bacterial genome. 17. Give any 3 proteins of fungi whose genome structure is elucidated. 18. Site out few fungi whose genomes are completely sequenced? 19. Site out few bacteria whose genomes are completely sequenced? 1. 2. 3. 4. 5. 6. 7. 8. 9. PART B Discuss in detail about COG Write detailed account on genome databases. Write detailed account on the goals and applications of HGP. Write detailed notes on KEGG. Discuss in detail about Fungi genome. Give a detailed account on bacterial genome. Explain the organization of Human Genome. Write an essay on Genomics in Agriculture Explain in detail about MBGD.

UNIT V Applications of Genomics PART-A 1. What is Exon shuffling? 2. Give the advantages of genetic marker. 3. Define Traits. 4. Write short notes on pharmacogenomics. 5. Define Proteomics. 6. What is gene knockout? 7. Define Ontology. 8. Write notes on polymorphism. 9. Define haplotype. 10. Define genotype. 11. Give the importance of Microsatellites. 12. What are minisatellites? 13. Define comparative genomics. 14. What are the advantages of comparative genomics? 15. Give the advantages of phylogenetic comparison. 16. Define Paralog. 17. Write notes on Ortholog. 18. Write short notes on Homology. 1. 2. 3. 4. 5. 6. PART B Illustrate the importance of genomics in bioinformatics What is horizontal gene transfer? Explain Write the applications of genomics in Bio-Pharmaceutical industry Explain genomic comparison at nucleotide level Discuss the impact of genomics on agriculture. What is comparative genomics? What are the methods of comparisons? Explain

7. Write a detailed account on ontological comparison. 8. Enumerate on phylogenetic comparison. 9. Discuss in detail how genomics plays a critical role in molecular diagnosis. 10. Explain the ontological comparison of genomes.

VINAYAKA MISSIONS UNIVERSITY AARUPADI VEEDU INSTITUTE OF TECHNOLOGY, PAIYANOOR & VMKV ENGINEERING OF COLLEGE, SALEM DEPARTMENT OF BIOINFORMATICS QUESTION BANK SUBJECT: MOLECULAR EVOLUTION AND PHYLOGENY CLASS/SEM: III/V REGULATION: 2006 UNIT I -Molecular Evolution PART-A 1. Define molecular evolution. 2. What is gene frequency? 3. Define positive selection. 4. Define co-dominant. 5. What is over dominance? 6. Define Random Genetic Drift. 7. Define Gene Substitution. 8. Define genetic polymorphism. 9. What is parallel substitution? 10. Define sequence similarity. 11. What is gene duplication? 12. What are the different types of gene duplication? 13. What is paraloguous? 14. Define orthologous. 15. What is Gene sharing? PART - B 1. Give detailed account on the population genetics. 2. Describe in detail about gene substitution. 3. Explain in detail about Dynamic gene population. 4. Write an essay of Natural selection. 5. Describe about Domain duplication and their type. 6. Give detailed account on Genetic Drift 7. Explain the history of molecular evolution in detail. 8. Differentiate homologous and homoplasious with suitable examples. 9. Define recombination. Explain its role in evolution. 10. Explain evolutionary changes in nucleotide sequences. UNIT II -Evolutionary Analysis PART - A 1. Define the rate of nucleotide substitution.

2. Define Coding Region. 3. Write a note on non-coding region with example? 4. Define poltploidy. 5. Define synonymous mutation. 6. What is non-synonymous region? 7. Define Neutral theory. 8. Write a note on Jukes-cantor model. 9. Define point mutation. 10. What is substitution? 11. Write a note on Allozymes. 12. Define mutation. 13. Define Transition. 14. Write a note on Transversion. 15. Define back mutation. PART - B 1. What is mutation? Explain its various types in detail. 2. Write notes on: a) Coding Region b) Non-Coding Region b) Transversion c) Base substitution 3. Write Short notes on: a) Transition b) Transversion c) Nucleotide substitution. 4. Explain genetic variation within species with suitable example. 5. Explain the model of molecular evolution. 6. Describe in detail about molecular clock. 7. Explain in detail about rate and pattern of nucleotide substitution. 8. Give detailed account on Genetic variation with in species. 9. Mutation plays a major role in molecular evolution Justify. 10. How is genes functions change by recombination? Explain UNIT III -Molecular Phylogenetics PART: A 1. 2. 3. 4. 5. 6. Define Phylogenetics (or) phylogeny. What are the different types of Phylogenetic trees? Differentiate Rooted and unrooted tree. What does the terminal and internal nodes represent? What is ultrametric tree? Define OUTs.

7. Write a note on Dendrogram. 8. Define Gene trees and species trees. 9. Explain Branch and node. 10. Draw a simple phylogenetic tree and give its nested paenthesis? 11. What is cladogram? 12. What are the types of phylogenetic tree based on resolution? 13. Write a note on clades. 14. Define Distances. 15. What are the methods involved in molecular Phylogenetics. PART - B 1. 2. 3. 4. 5. 6. 7. 8. 9. Write an essay of molecular Phylogenetics. Give detailed account on Phylogenetic trees. Distinguish between Phylogram & Cladogram Write detailed account on archeology of Molecular Phylogenetics. What is metric distance? Explain its types. Compare paraloguous and orthologous in detail. Give detailed account on gene tree and species tree. Write detailed account on molecular Phylogeny with example Write Short notes on a) Phylogenetics b) Rooted Tree c) Unrooted Tree 10. Write brief notes on a. Monophyletic groups b. Clades UNIT IV -Phylogeny Algorithms PART A 1. Define Transversion 2. Define translation. 3. What is dotplot? 4. What is homology? 5. What is homoplasious? 6. Define orthologous genes. 7. What is distance correction? 8. Define pralogous genes. 9. Name the methods used to construct a phylogenetic tree. 10. What is cost of alignment? 11. What is the principle behind maximum parsimonious method? 12. What is the principle behind maximum likelihood method? 13. Give a short note on possible substitutions among the four nucleotides. 14. What is gap penalty?

15. Which is called as phylogenetically uninformative site? PART B 1. 2. 3. 4. Explain in detail about Maximum parsimony mehod. How is distance method helping us to construct a phylogenetic tree? How Maximum likelihood constrcts a phylogenetic tree? What are the different models useful to estimate a nucleotide subatitutions among a pair of DNA sequences? How are they interrelated to each other? 5. What is substitution? Explain its various types with suitable example. 6. What is sequence alignment? How will you align the given two nucleotide sequences using dotplot? 7. Explain the problems encountered with the protein sequence alignment. 8. How will you identify consensus sequence and ancestor sequence from the given sequences? Explain 9. Discuss about problems associated with Phylogenetic reconstruction. 10. How will you measure evolutionary change? Explain UNIT V-Evolutionary Tree PART - A 1. Write a note on PHYLIP 2. Define PAPU 3. What is PUZZLE? 4. Define MACLADE 5. What is MOLPHY? 6. Name few internet accessible phylogenetic analysis softwares. 7. Name few packages of phylip. 8. Define Tree View 9. Name one rooted and unrooted tree drawing program. 10. What is Species tree? 11. Mention any two applications of molecular phylogeny. 12. Name few packages of PHYLIP used for protein sequence analyses. 13. Write a note on ClustalW. 14. What is DNAML? 15. Name few packages of PHYLIP used for DNA sequence analysis. PART - B 1. Give a brief account on PHYLIP 2. Explain any one software used for construction of a phylogenetic tree for nucleotide sequences.

3. Explain any one software used for construction of a phylogenetic tree for protein sequences. 4. Describe about phylogenetic tree analyzing softwares. 5. Explain in detail about application of phylogenetics. 6. Explain about the various Internet-Accessible phylogenetic analysis software. 7. What are the merits and demerits of various Internet-Accessible phylogenetic analysis software. 8. Point out the importance of phylogenetic analysis. 9. Write an essay on molecular evolution. 10. Write a notes on a) Gene tree b) Species tree.

VINAYAKA MISSIONS UNIVERSITY AARUPADAI VEEDU INSTITUTE OF TECHNOLOGY, PAIYANOOR & VMKV COLLEGE OF ENGINEERING, SALEM DEPARTMENT OF BIOINFORMATICS QUESTION BANK SUBJECT: PERL FOR BIOINFORMATICS YEAR/SEM: III/V REGULATION: 2006 Unit 1 Introduction to UNIX PART-A 1. Define operating system. Give examples. 2. Write short notes on GNU project. 3. List out benefits of Linux. 4. What are the hardwares and recommended hardware requirements for installing Linux? 5. Give brief account of Root. 6. Give brief account on absolute path. 7. Write notes on relative path. 8. How will you list the content of a directory? 9. Discuss about file creation command. 10. What command is used for viewing text? 11. How will you copy files and directories? 12. Give brief notes on creating and removing of files & directories. 13. What is lib directory? 14. Discuss the use of pwd command 15. What is function of cd command? PART-B Discuss the history of UNIX and its concept. Write detailed notes on Free Software Foundation and GNU project Explain the history of Linux and its benefits. Describe the Linux hierarchy file system. Write brief notes on a) Create directories b) Subdirectories c) Files. 6. What is path? Classify the types and explain with examples 7. Explain the following commands with examples a) cd b) ls c) cp e) rm f) mkdir 8. Write short notes on a) root directory 1. 2. 3. 4. 5.

b) usr directory c) bin directory d) boot directory e) tmp directory f) etc directory 9. Discuss about creating directories & sub directories and commands used 10. Explain about commands used to removing directories & subdirectories with suitable examples Unit 2 UNIX Essential PART-A 1. Give brief account on shell in UNIX 2. Define bash shell. 3. Write notes on command line history. 4. Discuss about command line editing. 5. Write short notes about UIDs and /etc/passwd file 6. Discuss about GIDs and /etc/group file 7. List out any five text processing software tools in UNIX 8. How will you move the curser in command line? 9. How will you save and exit from Vi editor? 10. Command line expansion 11. Write about yanking and putting text. 12. Give short notes on text files 13. Discuss about binary files 14. How will you create new files using Vi editor? 15. How the texts can be deleted in Vi Editor and which command is used? PART-B What is shell? Explain about Bash shell. Explain about command line expansion and protecting from expansion in detail. Write the various steps involved in command line editing. Explain in brief about Users, Groups, UIDs and GIDs Discuss about root user, and security in UNIX List out few text editors and explain in brief about Vi editor Describe about Vi editors three different modes and commands Differentiate the input mode and command mode Explain the following a) Beginning vi editor from terminal b) Creating files c) Switching input mode to command mode d) List of commands used in command mode e) Adding text from another file 10. Write notes for following f) Undoing changes 1. 2. 3. 4. 5. 6. 7. 8. 9.

g) h) i) j)

Searching and replacing Copying and pashing Saving and exiting a file Viewing the file contents

Unit 3 Introduction to Perl PART-A 1. List out the Perl components. 2. Give brief account on history of Perl. 3. What are the features of Perl? 4. Define variables. List the different types of variables. 5. Write short notes on scalar variable. 6. Discuss about array variable with examples. 7. What is hash variable? Give examples. 8. Write short notes on arithmetic operator. 9. Give brief account on logical operator. 10. What is a statement? 11. Define Loop. What types of loops are available in perl? 12. What is regular expression? 13. Write short notes on cmp operator. 14. Differentiate if and unless statements. 15. What is while loop? Give suitable examples. PART-B 1. Discuss about perl components. 2. Define variable. List and explain about the variables in Perl. 3. Define control statements and Discuss with examples 4. Explain loops with suitable examples. 5. What is file handle? Describe about file handle functions 6. Explain about file handles 7. Discus about perl parsing rules 8. How will you transcript and translate a DNA sequence 9. Define operators. Explain with examples 10. Discuss about Regular expression Unit 4 Features in Perl PART-A 1. 2. 3. 4. 5. What is Chomp function? Give examples Write short notes on join function. How will works split function? Discuss about ref function. Give brief account on time function.

6. What is socket module? 7. Write short notes on error checking. 8. Give short notes on arrays of hashes. 9. Write notes on hashes of hashes. 10. What is slice? Give examples. 11. Give brief account on shift. 12. Discuss about unshift function. 13. Give an account onpush. 14. Give examples for pop function 15. Write short notes on reverse function. PART-B 1. Explain the data manipulations with suitable examples 2. Explain the following functions with example a) Abs b) Int c) Exp d) Sqrt e) Log f) Trigonometric functions 3. Write short notes about the following functions with examples a) time b) sleep c) alarams 4. What is the data manipulation functions used in strings? Explain 5. Explain the functions used for error checking. 6. Explain the complex data structure with examples. 7. Write brief notes about socket module 8. Discuss about DBM databases and classify the types 9. How the Win32::ODBC module is used? Explain 10. Define the sub routines. How will you create using sub routines? Explain Unit 5 Enhancement of Perl PART-A 1. 2. 3. 4. 5. 6. 7. 8. 9. Define widgets. Give brief account of label widgets. Write short notes Button widgets. Discuss about text widgets. Give brief note on menu button widgets. Define HTML. What is CGI? Give brief account on URL What are cookies?

10. Write short notes on Bio Perl. 11. Give examples for concatenating DNA fragment. 12. Define transcription 13. What is translation? 14. How will you count nucleotides? 15. What is binding operator? PART-B 1. Explain briefly about widgets 2. Write short notes on a) Check b) Text c) List boxes d) Menus 3. How does the common gateway interface works? Explain 4. Discuss the applications of perl in biology 5. Elaborate bioperl application in bioinformatics 6. Write a perl programme for GC counting. 7. Write a perl programme for convert DNA sequence to protein sequence 8. Discuss about Tk and the installation of Tk in UNIX and Windows 9. Write a brief notes about widgets 10. Explain about extending and embedding perl