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Well-structured and detailed explanation of Greedy Algorithms: Genome Rearrangements, Sorting

by Reversals, Finding Motifs. suitable for answering a 30-mark exam question answering for subject
computational biology. Cover all essential aspects, including introduction, key concepts, formulas,
derivations, applications, advantages, limitations, and relevant diagrams or charts for clarity.
Information should be concise yet exhaustive bro keep it simple and as per msc level but the
content should be well detailed elaborate more stop giving just headings

Exhaustive Search: Restriction Mapping, Finding Motifs.

Greedy Algorithms: Genome Rearrangements, Sorting by Reversals, Finding Motifs.
Divide-and-Conquer Algorithms: Divide-and-Conquer Approach to Sorting, Space-Efficient Sequence
Alignment, Block Alignment.
Unit - III

Hidden Markov Models: Markov processes and Markov Models, Hidden Markov Models, Parameter
estimation for HMMs, Optimal model construction, Applications of HMMs.
Artificial Neural Networks: Historic evolution – Perceptron, NN Architecture, supervised and
unsupervised learning, Back Propagation Algorithm, Training and Testing, Self-organizing Feature
Map and Radial Basis Function Network; Overview of Support Vector Machines, Bayesian network.

Unit - IV

Clustering and Trees: Hierarchical Clustering, K-Means Clustering, Evolutionary Trees, Distance-Based
Tree Reconstruction, Reconstructing Trees from Additive Matrices, Character-Based Tree
Reconstruction, Small and Large Parsimony Problem.

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Well-structured and detailed explanation of structure and function of antibody molecules suitable
for answering a 30-mark exam question. Cover all essential aspects, including introduction, key
concepts, formulas, derivations, applications, advantages, limitations, and relevant diagrams or
charts for clarity. Information should be concise yet exhaustive bro keep it simple and as per msc
level but the content should be well detailed elaborate more stop giving just headings
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Unit - I

Innate and adaptive immune system: Cells and molecules involved in innate and adaptive immunity,
antigens, antigenicity and immunogenicity. B and T cell epitopes, structure and function of antibody
molecules.
Generation of antibody diversity, monoclonal antibodies, antibody engineering, antigen-antibody
interactions, MHC molecules, antigen processing and presentation, activation and differentiation of B
and T cells, B and T cell receptors.

Unit - II

Humoral and cell-mediated immune responses, primary and secondary immune modulation, the
complement system, Toll-like receptors, cell-mediated effector functions, inflammation,
hypersensitivity and autoimmunity.
Immune response during bacterial (tuberculosis), parasitic (malaria) and viral (HIV) infections,
congenital and acquired immunodeficiencies, vaccines.

Unit - III

Isolation and purification of RNA, DNA (genomic and plasmid) and proteins, different separation
methods. One- and two-dimensional gel electrophoresis, Isoelectric focusing.
Molecular cloning of DNA or RNA fragments in bacterial and eukaryotic systems.
Expression of recombinant proteins using bacterial, animal, and plant vectors. Isolation of specific
nucleic acid sequences. Generation of genomic and cDNA libraries in plasmid, phage, cosmid, BAC
and YAC vectors.

Unit - IV

In vitro mutagenesis and deletion techniques, gene knockout in bacterial and eukaryotic organisms.
Protein sequencing methods, detection of post-translational modification of proteins.
DNA sequencing methods, strategies for genome sequencing.
Methods for analysis of gene expression at RNA and protein level, large-scale expression, such as
microarray-based techniques, RFLP, RAPD, and AFLP techniques.

This syllabus is for M.Sc. Bioinformatics at Maharshi Dayanand University Rohtak (Session 2024-25).

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Well-structured and detailed explanation of . building search protocol. for advance bioinformatics
suitable for answering a 30-mark exam question. Cover all essential aspects, including
introduction, key concepts, formulas, derivations, applications, advantages, limitations, and
relevant diagrams or charts for clarity. Information should be concise yet exhaustive bro keep it
simple and as per msc level but the content should be well detailed elaborate more stop giving just
headings elaborate more and keep language simple

Here is the text from the image:

Unit - I

DNA sequence analysis: Pairwise alignment techniques, Global and local alignments; Algorithms;
Scoring Matrices, Gap penalties, and Statistical significance. Tools of sequence alignment: FASTA;
BLAST and its variations; Multiple sequence alignment; Tools – CLUSTAL; MUSCLE; T-Coffee.

Unit - II

Protein sequence analysis: BLAST-P; PROSITE; Pfam; CATH; SCOP

Secondary database searching, building search protocol.
Computer-aided drug design – Basic principles, protein modeling, and design.

Unit - III
Pharmacogenomics: Introduction, applications, Genome for medicine, current and future
perspectives.
Metagenomics: Introduction; concepts; Applications in clinical research; environmental research;
etc.
Phylogenomics: Basic principle and applications.

Unit - IV

Analysis packages – Commercial databases and packages, GPL software for Bioinformatics, web-
based analysis tools. System modeling and metabolomics – concepts and principles.

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Well-structured and detailed explanation of . Genome databases of Plants, animals, and pathogens
answer should be around subject genomics and proteomics suitable for answering a 30-mark exam
question. Cover all essential aspects, including introduction, key concepts, formulas, derivations,
applications, advantages, limitations, and relevant diagrams or charts for clarity. Information should
be concise yet exhaustive bro keep it simple and as per msc level but the content should be well
detailed elaborate more stop giving just headings elaborate more and keep language simple
nit - I

Genomics: Introduction to the concept of genome, gene networks: basic concepts, Prediction of
genes, promoters, splice sites, regulatory regions: basic principles, application of methods in genome
projects. Human Genome Project. Large-scale genome sequencing strategies, Genome assembly and
annotation. Genome databases of Plants, animals, and pathogens.
Metagenomics: Concept and applications.

Well-structured and detailed explanation of , synteny and gene order comparisons answer should be
around subject genomics and proteomics suitable for answering a 30-mark exam question. Cover all
essential aspects, including introduction, key concepts, formulas, derivations, applications,
advantages, limitations, and relevant diagrams or charts for clarity. Information should be concise yet
exhaustive bro keep it simple and as per msc level but the content should be well detailed elaborate
more stop giving just headings elaborate more and keep language simple

Unit - II

Comparative genomics: Basic concepts and applications, Whole genome alignments: understanding
the significance; Artemis, BLAST2, MegaBlast algorithms, PipMaker, AVID, Vista, MUMmer,
applications of suffix tree in comparative genomics, synteny and gene order comparisons.
Comparative genomics databases: COG, VOG.
Epigenetics: DNA microarray: database and basic tools, Gene Expression Omnibus (GEO),
ArrayExpress, SAGE databases: understanding of microarray data, normalizing microarray data,
detecting differential gene expression, correlation of gene expression data to biological processes
and computational analysis tools (especially clustering approaches).

Conduct a comprehensive analysis of the VOG tool/ website, focusing on its role as a tool for
genomics and proteomics research. Evaluate the following aspects in detail:

🔬 Scientific Utility & Features:

 Describe its core functionalities and how it aids in genomics/proteomics research.

 Assess its accuracy, reliability, and computational efficiency.

 Mention any algorithms, machine learning models, or bioinformatics techniques it uses.

⚙️User Experience & Accessibility:

 Examine the website’s interface, ease of navigation, and overall user-friendliness.

 Specify if it requires coding knowledge or provides graphical tools for non-coders.

 Check whether the tool is free, freemium, or paid and if registration is required.

📊 Data Integration & Compatibility:

 Determine whether it supports data upload, download, and sharing.

 Assess compatibility with formats like FASTA, VCF, BAM, or others.

  Identify if it integrates with databases like NCBI, Ensembl, UniProt, etc.

🔍 SEO & Discoverability:

 Evaluate its search engine ranking and visibility among bioinformatics researchers.

 Check for citations in scientific papers and mentions in academic discussions.

🔐 Security & Trustworthiness:

 Assess HTTPS/SSL encryption and user data privacy policies.

 Identify any potential cybersecurity risks or vulnerabilities.

📈 Performance & Technical Aspects:

 Analyze loading speed, mobile compatibility, and uptime reliability.

 Check if the tool supports cloud-based analysis or local installation.

🌍 Scientific Reputation & Community Engagement:

 Look into citations, institutional backing, and user reviews.

 Identify if there is an active forum, GitHub repository, or scientific community around it.

✅ Advantages:

 List its major benefits over other similar tools.

 Highlight unique features that make it stand out.

❌ Disadvantages:

 Mention any limitations, errors, or drawbacks.

 Identify potential challenges users might face.

Applications & Use Cases:

 Describe how researchers, students, or professionals use the tool.

 Provide real-world scenarios where it is applied in genomics/proteomics studies.

🌐 Availability & Access:

 Mention where the tool can be accessed (website link, GitHub, institutional login, etc.).

 Check if it has a downloadable version, API access, or mobile compatibility.

Provide a structured breakdown of findings, including strengths, weaknesses, and recommendations

for improvement

Unit - III
Proteomics: Concept of proteome, protein array, Methods of protein analysis: PAGE (Native, SDS),
Mass Spectrometry, X-ray crystallography, nuclear magnetic resonance (NMR), Deriving function
from sequence, Proteomics in drug discovery and toxicology.

Unit - IV

Metabolomics: Introduction to metabolomics, technology in metabolomics, structure and evolution

of biological networks, Importance of metabolic engineering, Metabolic pathway databases (EcoCyc,
MetaCyc, LIGAND, ENZYME, BRENDA, KEGG).