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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:
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 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
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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:
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 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
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Automated DNA sequencing
Traditional methods of
manual DNA sequencing
utilize radioactive isotopes
to label the DNA.
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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
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through gene expression profiling:
 Leukemia:
 Oral cancer,
 Lung cancer
*A-Answer
Note –Please provide keywords, short answer, specific terms, specific examples (wherever necessary)
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