VALLIAMMAI ENGINEERING COLLEGE

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1 VALLIAMMAI ENGINEERING COLLEGE SRM Nagar, Kattankulathur DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING QUESTION BANK VII SEMESTER BM6005 BIO INFORMATICS Regulation 2013 Academic Year Prepared by Dr.L.Karthikeyan AP (Sr.G)/CSE

2 VALLIAMMAI ENGINEERING COLLEGE SRM Nagar, Kattankulathur DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING SUBJECT SEM / YEAR: VII/VI : Bio informatics QUESTION BANK UNIT I INTRODUCTION Need for Bioinformatics technologies Overview of Bioinformatics technologies Structural bioinformatics Data format and processing Secondary resources and applications Role of Structural bioinformatics - Biological Data Integration System. PART A Q.No Questions BT Level Competence 1. Define Bioinformatics. 2. Describe the two major challenges in the area in the bioinformatics. 3. Explain the different types of database. 4. Define Gene prediction. 5. State the technologies within the Bioinformatics. BTL-3 Apply 6. Explain structure analysis. 7. Describe the key components of PDB. BTL-2 Understand 8. What is PDB format? BTL Differentiate the structure alignment CE and DALI. 10. Prepare and write concept of DIP BTL-6 Create 11. Give the details of secondary resources. BTL-2 Understand 12. Explain the structural domain CATH classifications. 13. Prepare and write the concept of DOCKING. BTL-6 Create 14. Define the Homology modelling. 15. Describe the ligand based design. 16. Give the list of visualization tool. BTL Differentiate the CATH, SCOP and DALI. 18. State the functional prediction. BTL-3 Apply 19. Give the details of computational approach. BTL-2 Understand 20. Examine the Biomoleculer interaction network database BTL-3 Apply PART B 1. i) Define the importance of information technology in Bio informatics.(6) ii) Describe the needs of Bio informatics technology.(7) 2. Discuss the overview of the Bio informatics technology.(13) BTL-2 Understand

3 3. Describe the conceptual organization of resource in structural bio informatics.(13) 4. i) Apply the concept of organization structure bioinformatics(7) BTL-3 Apply ii) write about the primary resources.(6) 5. i)explain the concept of secondary resources (6) ii)explain its application.(7) 6 Assess the concept of structural comparisons (alignment).(13) 7 Discuss in details about the structural classification.(13) BTL-2 Understand 8 Point out the techniques handled in structure prediction.(13) 9 i) Develop and shows the roles informatics plays in the post genomic drug discovery. (8) ii) Design preclinical drug discovery process with neat diagram (5) BTL-6 Create 10 Examine the Functional Assignments in Structural Genomics.(13) 11 Analyze the concept of protein-protein interaction.(13) 12 Express in details of protein-ligrand interaction.(13) BTL-2 Understand 13 Describe Computational approaches used for inferring protein-protein interactions.(13) 14 Solve the Role of Structural Bioinformatics in Systems Biology.(13) BTL-3 Apply PART-C 1 Analyze the visualization tools in the bio informatics filed.(15) 2 (i) Summarize the concept of database for integrating protein (DIP).(10) (ii) Describe in details about Family-depended conservation (5) 3 Formulate the BIND in protein-protein interaction.(15) BTL-6 Create 4 Deduce the concept of gene Fusion.(15)

4 UNIT II DATAWAREHOUSING AND DATAMINING IN BIOINFORMATICS Bio informatics data Data warehousing architecture data quality Biomedical data analysis DNA data analysis Protein data analysis Machine learning Neural network architecture and applications in bioinformatics. PART A Q.No Questions BT Level Competence 1 List the bioinformatics database. 2 Tabulate the information about error and discrepancies. 3 Deduce the KDD. 4 What is bioinformatics data? 5 Apply the data mining concept in bio informatics. BTL-3 Apply 6 Explain the four module of DNA database. 7 Illustrate the DNA component. BTL-3 Apply 8 Define Data quality. BTL -1 9 Differentiate the EMBL and GenBank. 10 Prepare the three major database for protein sequence. BTL-6 Create 11 Give the three steps of transcription. BTL-2 Understand 12 Differentiate the prokaryotes and eukaryotes 13 Develop the example of helix structure of DNA. BTL-6 Create 14 Define transcription. 15 Define the three layer feed forward neural network. 16 Discuss the machine learning and the three phases. BTL-2 17 Explain the neuron model. 18 Discuss the average mutual information. BTL-2 Understand 19 Express the Alignment tools for protein sequence. BTL-2 Understand 20 Show the general structure of amino acid. BTL-3 Apply PART B 1 i) Describe the nature of biological data and problems frequently encountered in managing them(8) ii) Draw the structure of a data warehouse.(5) 2 i) Express data warehousing principles and the basic architecture of a biological data warehouse.(7) ii) Design the Conceptual map of data warehousing process.(6) BTL-2 Understand 3 Describe the transforming data into knowledge using data warehousing.(13) 4 Solve the data quality in area of bio informatics.(13) BTL-3 Apply

5 5 i) Explain the three DNA sequence database.(6) ii) Explain the three databases for protein sequence. (7) BTL-4 Analyze 6 i) Explain the software tool that facilitate research in bio informatics.(7) ii) Design the helix of DNA sequence and explain it(6). 7 i) Discuss the sequence comparison and alignment.(7) ii) Design the general structure of amino acid.(6) BTL-2 Understand 8 i) Compare the protein sequences.(6) ii) Analyse the seven protein classes in SCOP.(7) 9 i) Develop the three layer neural network and explain it.(7) ii) Implement the Machine learning in Bioinformatics that research area.(6) 10 Examine the protein structure comparison(13) BTL-4 BTL-6 Analyze Create 11 Explain the neuron model architecture.(13) 12 Discuss Biological neural network and explain it.(13) BTL-2 Understand 13 Describe the training of neural network.(13) 14 Demonstrate the genetic algorithm in bio informatics.(13) PART-C BTL-3 Apply 1 Design your own DNA helix structure and explain it.(15) 2 Summarize the software tools which can be used in protein analysis.(15) 3 Design the neural network for simple calculator.(15) BTL-6 Create 4 Create the machine learning implementation in the bio informatics field.(15)

6 UNIT III MODELING FOR BIOINFORMATICS Hidden Markov modeling for biological data analysis Sequence identification Sequence classification multiple alignment generation Comparative modeling Protein modeling genomic modeling Probabilistic modeling Bayesian networks Boolean networks - Molecular modeling Computer programs for molecular modeling. PART A Q.No Questions BT Level Competence 1. List the three primary of HMM bio logical area 2. What is target sequence? 3. Deduce the TATA box. 4. Define the hierarchical framework for identification 5. Show the flowchart involved in the short sequence identification method. BTL-3 Apply 6. Explain the HMM form analysis. 7. Examine the sample HMM profile. BTL-3 Apply 8. List the major steps used in PHMM generation. BTL Point out the Viterbi algorithm. 10. Design the steps involved in the Viterbi algorithm. BTL-6 Create 11. Develop the steps to be followed to create an experimental framework for protein comparative BTL-6 Create modelling. 12. Design the Boolean cell regulation representation. 13. Distinguish the comparative modelling servers. BTL-2 Understand 14. Define comparative genomics List the two levels of comparative genomics 16. Explain the Bayesian network. BTL Differentiate the program for molecular mechanics. 18. Describe the SCFG. BTL-2 Understand 19. Discuss the different gene expression. BTL-2 Understand 20. Show the basic unit of probabilistic Boolean network. BTL-3 Apply PART B 1 Describe the Hidden Markov Modeling for Sequence Identification. (13) 2 Design Hidden Markov Modeling for Sequence classification.(13) 3 Describe Hidden Markov Modeling for Multiple Alignment Generation (13) 4 i)illustrate Flow Chart for Short Target Sequence Model Development(7) ii)demonstrate the HMM form analysis.(6) 5 i) Explain the concept of protein comparative modelling.(6) ii) Explain in detail the comparative genomic modelling.(7) BTL-2 BTL-3 BTL-4 Understand Apply Analyze

7 6 i) Compare the protein and genomic modelling.(7) ii) Summarize the probabilistic modelling.(6) 7 Discuss the Probabilistic Boolean Networks.(13) BTL-2 Understand 8 Write and Analyse the concept of Molecular and Related Visualization Applications.(13) BTL-4 Analyze 9 Design and development of the following visualization BTL-6 Create techniques: 1. Scatter plots(4) 2. Heat maps(3) 3. Multidimensional(3) 4. Anatomical mapping(3) 10 i)design the key steps for multiple alignment(7) ii) Explain it.(6) 11 Write about Differential gene expression(13) 12 Implement the software in the molecular BTL-2 Understand modelling.(13) 13 Describe about molecular mechanics.(13) 14 Analyze the following i) Homologous Enzymes 1QCQ (6) ii) Homologous Enzymes 2AAK(7) BTL-3 Apply PART-C 1. Analyse the HMM data with realistic data.(15) 2. Assess the detail about comparative modelling with any realistic data.(15) 3. Design the Bayesian network with real time environment. (15) BTL-6 Create 4. Design and explain the software used in molecular modelling.(15) UNIT IV

8 PATTERN MATCHING AND VISUALIZATION Gene regulation motif recognition motif detection strategies for motif detection Visualization Fractal analysis DNA walk models one dimension two dimension higher dimension Game representation of Biological sequences DNA, Protein, Amino acid sequences. PART A Q.No Questions BT Level Competence 1 Define motif. 2 Name the Transcription factors 3 Compare the two classes of promoters 4 Define Motif recognition 5 Show the consensus pattern BTL-3 Apply 6 Explain probability matrix 7 Illustrate phylogenetic profiling. BTL-3 Apply 8 List the two major approaches to increasing the statistical power of pattern recognition motif searching algorithms. BTL -1 9 Pointout the central dogma. 10 Design the DNA controls the biological functions BTL-6 Create 11 Classify the kinds of amino acids are found in proteins. BTL-2 Understand 12 Differentiate 13 Generalize the genetic code. BTL-6 Create 14 Define polypeptides. 15 What is detailed HP model? 16 Summarize the attractor of the IFS BTL-2 17 Explain the fractal. 18 Distinguish one dimension and two dimension DNA model BTL-2 Understand 19 Give the higher dimension DNA. BTL-2 Understand 20 Show the chaos game. BTL-3 Apply PART B 1 i) List the motif detection strategic (6) ii) Describe the Gene Regulation. (7) 2 Discuss the Motif Recognition.(13) BTL-2 Understand 3 Examine the Recurrent Iterated Function System Model.(13) 4 Demonstrate the Moment Method to Estimate the Parameters of the IFS.(13) BTL-3 Apply 5 i) Explain Multiracial Analysis (6) ii) Explain One-Dimensional DNA Walk.(7) 6 Assess the Two-Dimensional DNA Walk.(15) 7 Discuss the Game Representation of DNA Sequences.(13) BTL-2 Understand

9 8 Pointout the Game Representation of Protein sequences.(13) 9 Design the Game Representation of Protein Structures.(13) BTL-6 Create 10 Describe Two-Dimensional Portrait Representation of DNA Sequences(13) 11 Design and analyze the Game Representation of Amino Acid Sequences Based on the Detailed HP Model.(13) 12 Discuss the Measure Representation of Complete Genomes.(13) 13 Describe the Measure Representation of Linked Protein Sequences (13) 14 Illustrate Measure Representation of Protein Sequences Based on Detailed HP Model (13) BTL-2 Understand BTL-3 Apply PART-C 1 Analyze the concept of Pattern Matching for Motifs(15) 2 Deduce the Fractal Analysis of Biological Sequences(15) 3 Generalize the Chaos Game Representation of Biological Sequences(15) BTL-6 Create 4 the Chaos Game Representation of Protein Structures (15) UNIT V MICROARRAY ANALYSIS Microarray technology for genome expression study image analysis for data extraction preprocessing segmentation gridding spot extraction normalization, filtering cluster analysis gene network analysis Compared Evaluation of Scientific Data Management Systems Cost Matrix Evaluation model - Benchmark Tradeoffs. PART A Q.No Questions BT Level Competence 1 Define Microarray deals. 2 Name hybridization technique. 3 Assess the steps involved in a cdna microarray experiment. 4 Define Block segmentation. 5 Apply Automatic Gridding. BTL-3 Apply 6 Explain Spot Extraction. 7 Illustrate Cluster Analysis BTL-3 Apply 8 List the main advantages of the BHC clustering algorithm. BTL -1 9 Point out Original gene expression data

10 10 formulate Expression data after BHC clustering BTL-6 Create 11 Express Self-Splitting and Merging Competitive Learning Clustering BTL-2 Understand 12 Infer one-prototype-take-one-clusters. 13 Generalize Singular Value Decomposition. BTL-6 Create 14 Define Genome expression 15 Tell about the cdna 16 Summarize background correction. BTL-2 17 infer data normalization? 18 How the data filtering in microarray. BTL-2 Understand 19 Interpret missing values estimation. BTL-2 Understand 20 Show the TIFF format. BTL-3 Apply PART B 1 Describe Microarray Technology for Genome Expression Study.(13) 2 Summarize the Image Analysis for Data Extraction.(13) BTL-2 Understand 3 Describe the Temporal Expression Profile Analysis and Gene Regulation.(13) 4 Apply Gene Regulatory Network Analysis.(13) BTL-3 Apply 5 Explain the schematic of the cdna microarray technique.(13) 6 Summarize image processing in microarray technique.(13) BTL-4 Analyze 7 Discuss about the Data normalization and filtering.(13) BTL-2 Understand 8 Analyze the missing value analysis. (13) 9 Formulate the BHC cluster analysis.(13) BTL-6 Create 10 Examine the benchmark for gene network analysis.(13) 11 Explain Compared Evaluation of Scientific Data Management Systems.(13) 12 Discuss the cost matrix for gene network analysis. (13) BTL-2 Understand 13 Describe the trade off about gene network analysis.(13) 14 Explain the evolution model for gene network analysis.(13) PART-C 1 Analysis the genome expression study with real time data.(15) 2 the DNA structure with multi array technique(15) 3 Design the your data with BHC cluster analysis(15) BTL-6 Create 4 Summarize the concept of gene network analysis(15)

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