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SMU-DDE-Assignments-Scheme of Evaluation PROGRAM SEMESTER SUBJECT CODE & NAME BK ID DRIVE MARKS Q. No 1 A 2 A MSC BIOINFORMATICS 3 BI0034 GENOMICS B0883 WINTER 2015 30 Criteria Marks Total Marks Explain the technique of microarray. Explain the steps involved in the detection of gene patterns in microarray data analysis. (Unit 2, Page No. 42 ) Brief description for the microarray technique: 3 10 A microarray is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to chemically suitable matrices. It is also called gene or genome chip, DNA chip, or gene array. Qualitative or quantitative measurements with DNA microarrays utilize the selective nature of DNA-DNA or DNA-RNA hybridization under high-stringency conditions and fluorophore-based detection. Explanation for the steps involved in the detection of gene patterns in 7 microarray data analysis1) Definition of a key gene and import / retrieval of the key gene sequence, 2) BLAST search of the key gene sequence against the local database, 3) Determination of the k neighboring genes at each side of the key gene, 4) All against all BLAST searches of the k neighboring genes, 5) Determination of orthologous genes using the reciprocal best hit approach and minimal triangle relationship, 6) Determination of gene patterns with a given minimal length and presence in at least q (quorum) different genomes providing systematic and heuristic search strategies, 7) Clustering and visualisation of gene pattern instances concerning gene order and direction together with their environmental parameters. The results of each process step are stored in the database and can be reiterated at each step with other parameters. Discuss the principle and working of Automated Fluorescence Sequencing. Explain how it differs from traditional methods of manual DNA sequencing. (Unit 1, Page No. 7) Explaining the principle of Automated Fluorescence Sequencing: 4 10 DNA sequencing method in which the radioactive labels, autoradiography, and manual base calling were all replaced by fluorescent labels; laser-induced fluorescence detection, and computerized base calling. Automated DNA sequencing utilizes fluorescent tracers instead of radioisotopes to label the DNA. Eliminates or significantly reduces the use of radioactive materials in some research laboratories. SMU-DDE-Assignments-Scheme of Evaluation Explaining the working of Automated Fluorescence Sequencing. The primer is labelled with one of the four different fluorescent dyes and each was placed in a separate sequencing reaction with one of the four dideoxynucleotides plus all four deoxynucleotides. Once the reactions are complete, the four reactions were pooled and run together in one lane of a polyacrylamide sequencing gel. The fluorescence signature of each fragment was then sent to a computer where the software was trained to perform base calling. The differences between Automated fluorescence sequencing and traditional methods of DNA sequencing: Traditional methods sequencing 4 2 Automated DNA sequencing Traditional methods of manual DNA sequencing utilize radioactive isotopes to label the DNA. 3 A Automated DNA sequencing utilizes fluorescent tracers instead of radioisotopes to label the DNA, thereby eliminating or significantly reducing the use of radioactive materials in some research laboratories. Manual DNA sequencing Automated deoxyribonucleic acid (DNA) produce considerable sequencing reduces the volume of low-level volume of radioactive radioactive waste, while providing a waste. suitable alternative to manual DNA sequencing. Explain the method of disease detection through gene expression profiling with suitable example. (Unit 3, Page No. 64) Explaining the method of detection of any one of the following diseases 10 10 through gene expression profiling: Leukemia: Oral cancer, Lung cancer *A-Answer Note –Please provide keywords, short answer, specific terms, specific examples (wherever necessary) ***********