Graduation Level Topics 

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1. Introduction to Biological Databases

Students learn how to access NCBI, EMBL, and UniProt for gene and protein information. Protocols include sequence retrieval, FASTA formatting, and BLAST search.

2. Protein Sequence Alignment Using BLAST

Protocols involve submitting protein sequences to BLASTp and analyzing homology. This is a standard practice in Indian bioinformatics labs.

3. DNA Sequence Alignment Using Clustal Omega

Protocols include multiple sequence alignment (MSA) of DNA sequences. Students analyze conserved motifs across species.

4. Retrieval of Protein Structures from PDB

Protocols involve searching the RCSB Protein Data Bank. Students learn visualization of 3D protein structures using PyMOL.

5. Primer Design for PCR

Protocols involve using Primer3 software to design primers for gene amplification. Applied in Indian molecular biology labs.

6. Phylogenetic Tree Construction Using MEGA Software

Protocols involve inputting aligned sequences and selecting neighbor-joining methods. Students study evolutionary relationships.

7. Gene Prediction Using Online Tools

Protocols involve uploading genomic sequences to GENSCAN or AUGUSTUS. Students identify exons and introns.

8. Protein Motif Analysis Using Pfam

Protocols involve scanning protein sequences for known motifs. Applied in functional annotation of uncharacterized proteins.

9. Secondary Structure Prediction of Proteins

Protocols involve running PSIPRED or SOPMA. Students compare predicted vs. experimental structures.

10. Retrieval of Human Genome Data from Ensembl

Protocols involve navigating Ensembl Genome Browser. Students learn about gene structure and chromosomal location.

11. Visualization of DNA Sequences Using SnapGene

Protocols involve importing gene sequences and annotating restriction sites. Students simulate cloning strategies.

12. Use of Swiss-Prot for Curated Protein Data

Protocols include searching protein entries, cross-references, and functional notes. Introduces students to curated bioinformatics datasets.

13. SNP Analysis Using dbSNP Database

Protocols involve retrieving polymorphism data for human or crop genes. Applied in Indian disease marker studies.

14. RNA Secondary Structure Prediction Using RNAfold

Protocols involve submitting RNA sequences and visualizing folding patterns. Useful in studying functional RNAs.

15. Codon Usage Analysis in Bacterial Genes

Protocols involve using CodonW software to analyze codon bias. Applied in recombinant protein expression.

16. Virtual Screening Basics Using PubChem

Protocols involve downloading ligands and preparing simple drug-target docking. This introduces students to cheminformatics.

17. Use of KEGG for Pathway Analysis

Protocols involve exploring metabolic pathways for specific enzymes. Indian labs use KEGG in crop and disease research.

18. Microarray Data Retrieval from GEO Database

Protocols involve downloading gene expression datasets from NCBI GEO. Students analyze differential expression.

19. Introduction to R for Bioinformatics

Protocols include basic R commands for data visualization and statistical analysis. Used widely in Indian research.

20. Identification of Restriction Sites in DNA Sequences

Protocols involve using NEBcutter for in-silico digestion. Students simulate molecular cloning experiments.

21. Genomic Data Mining Using UCSC Genome Browser

Protocols include browsing genes, SNPs, and regulatory elements. Students learn integrative genome analysis.

22. Molecular Docking Using AutoDock (Demonstration)

Protocols involve preparing a protein and ligand, running docking, and analyzing binding affinity. Introduced as a practical demo in Indian colleges.

23. Protein Domain Analysis Using InterProScan

Protocols involve uploading protein sequences for conserved domain search. Useful in functional annotation.

24. Comparative Genomics Using OrthoDB

Protocols involve identifying orthologous genes across species. Introduces students to evolutionary genomics.

25. Use of STRING Database for Protein-Protein Interactions

Protocols involve uploading proteins to STRING and visualizing interaction networks. Applied in Indian biomedical projects.

26. In-Silico PCR Simulation

Protocols involve using UCSC In-Silico PCR tool. Students validate designed primers computationally.

27. MicroRNA Target Prediction Using TargetScan

Protocols involve uploading mRNA sequences to predict miRNA interactions. Introduces students to regulatory RNA biology.

28. Gene Ontology (GO) Analysis Using AmiGO

Protocols involve browsing gene annotations based on biological processes. Students learn about gene function classification.

29. Comparative Transcriptome Analysis (Introductory)

Protocols involve retrieving transcriptome datasets and comparing expression levels. Provides exposure to NGS data.

30. Protein Hydrophobicity Analysis Using ProtScale

Protocols involve analyzing amino acid sequences for hydropathy profiles. Used for membrane protein prediction.

31. Basic Python for Bioinformatics

Protocols involve writing scripts for sequence handling (FASTA parsing, GC content). Introduces programming in biology.

32. Homology Modeling Using Swiss-Model

Protocols involve uploading protein sequences and generating 3D structures. Useful for studying unknown proteins.

33. Sequence Data Quality Check Using FASTQC

Protocols involve assessing raw NGS data for quality. Students practice bioinformatics preprocessing.

34. RNA-Seq Workflow (Demonstration)

Protocols involve aligning RNA-Seq reads to a reference genome. Introduced as a demo in Indian PG-level labs but simplified for graduates.

35. Antigenic Epitope Prediction for Vaccines

Protocols involve using IEDB tools to identify antigenic peptide sequences. Students study computational vaccinology.

36. Identification of Tandem Repeats Using TRF

Protocols involve submitting DNA sequences to detect repeats. Used in genetic marker development.

37. Genomic Variation Analysis Using Ensembl VEP

Protocols involve uploading SNP/INDEL data for effect prediction. Introduces students to variant annotation.

38. Sequence Logo Creation Using WebLogo

Protocols involve visualizing conserved motifs from MSA. Students interpret DNA/protein motif patterns.

39. Phylogenetic Analysis of Indian Crop Varieties

Protocols involve sequence alignment of Indian rice or wheat varieties. Useful in biodiversity studies.

40. In-Silico Restriction Mapping for Plasmids

Protocols involve simulating restriction digests for cloning vectors. Students understand lab-to-digital integration.

41. Protein Solubility Prediction for Recombinant Expression

Protocols involve using SOLpro or Protein-Sol tools. Students learn about protein design challenges.

42. Visualization of Protein-Ligand Complexes

Protocols involve using Chimera or PyMOL to analyze docking outputs. Students explore 3D molecular interactions.

43. Genome Assembly Basics Using Velvet (Demo)

Protocols involve short-read data assembly using simple tools. Students understand how genomes are reconstructed.

44. Calculation of GC Content in Genomes

Protocols involve writing scripts or using online tools. Applied in genome characterization projects.

45. Predicting Allergenicity of Proteins

Protocols involve using AlgPred tool to assess allergenicity. Introduced in food biotechnology studies in India.

46. In-Silico Identification of SSR Markers

Protocols involve mining genome sequences for simple sequence repeats. Useful for crop breeding projects.

47. Protein Stability Prediction Using I-Mutant

Protocols involve predicting stability change upon mutation. Students relate mutations to disease models.

48. Use of ExPASy for Protein Analysis

Protocols involve using ProtParam for molecular weight, pI, and hydrophobicity. Basic computational protein biochemistry exercise.

49. Docking of Herbal Compounds Against Human Targets

Protocols involve selecting phytochemicals from PubChem and docking against disease proteins. Relevant for India’s herbal drug research.

50. Introduction to Machine Learning in Bioinformatics (Demo)

Protocols involve classifying gene expression datasets using Weka. Students gain basic exposure to AI in biology.

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Post-Graduation Level Topics

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1. Genome-Wide Association Studies (GWAS) in Crops

Protocols involve SNP genotyping, statistical association testing, and Manhattan plot visualization. Indian labs apply GWAS in rice, wheat, and chickpea for trait discovery.

2. Next-Generation Sequencing Data Analysis Pipelines

Protocols include quality check with FASTQC, alignment with HISAT2, and variant calling with GATK. Widely used in India’s genome projects.

3. Metagenomic Analysis of Human Gut Microbiome

Protocols involve shotgun sequencing and taxonomic classification with Kraken2. Indian studies link gut microbiome to lifestyle disorders.

4. Structural Bioinformatics of SARS-CoV-2 Proteins

Protocols involve molecular dynamics simulations of spike protein and ACE2 interactions. Indian researchers contributed to COVID-19 drug repurposing.

5. Single-Cell RNA-Seq Data Analysis

Protocols include Seurat clustering, UMAP visualization, and differential expression analysis. Used globally and in India for immune system studies.

6. Protein-Ligand Docking and Virtual Screening

Protocols involve preparing large compound libraries, docking with AutoDock Vina, and ranking based on binding affinity. Applied in Indian herbal drug discovery.

7. CRISPR Guide RNA Design Tools

Protocols involve using CRISPR-Cas9 design servers (CHOPCHOP, CRISPOR) and off-target prediction. Applied in Indian labs for crop and livestock editing.

8. Systems Biology of Cancer Pathways

Protocols include network reconstruction using Cytoscape and flux balance analysis. Indian bioinformatics groups use these for drug target identification.

9. Deep Learning for Protein Structure Prediction

Protocols involve training neural networks on amino acid sequences. Inspired by AlphaFold, Indian researchers explore AI-based protein prediction.

10. Comparative Genomics of Indian Indigenous Breeds

Protocols include pan-genome construction and synteny analysis. Helps conserve biodiversity in livestock and crops.

11. Epigenomics Data Analysis Using ChIP-Seq

Protocols involve peak calling with MACS2 and annotation with HOMER. Indian groups use epigenomics to study stress adaptation in crops.

12. RNA Editing Analysis in Plant Genomes

Protocols involve aligning RNA-Seq reads to genomes and detecting nucleotide changes. Applied in rice and millets in India.

13. Quantum Computing in Molecular Docking (Emerging)

Protocols involve simulating protein-ligand interactions on quantum processors. Still emerging but gaining global attention.

14. Integrative Omics for Personalized Medicine

Protocols involve combining genomics, transcriptomics, proteomics, and metabolomics. Indian biotech start-ups explore this for cancer precision medicine.

15. Genome Annotation Using MAKER Pipeline

Protocols involve ab initio prediction, homology evidence, and transcript data integration. Applied in Indian draft genome projects.

16. Artificial Intelligence in Drug Repurposing

Protocols involve training ML models on drug-target interaction datasets. Used in India for COVID-19 and tuberculosis drug research.

17. Molecular Dynamics (MD) Simulations of Proteins

Protocols include setting up simulations with GROMACS, equilibration, and trajectory analysis. Used for stability analysis of drug-bound proteins.

18. Pan-Genome Analysis in Crops

Protocols involve building core and dispensable gene sets. Indian agricultural genomics centers use this for chickpea and pigeon pea.

19. Network Pharmacology of Ayurvedic Compounds

Protocols involve mapping herbal compounds to protein targets using Cytoscape. Applied in India’s AYUSH drug validation programs.

20. Artificial Neural Networks for Protein Folding

Protocols involve feeding amino acid features to ANN models. A frontier field combining computation and structural biology.

21. Next-Generation CRISPR Off-Target Prediction

Protocols involve computational scanning of genomes for off-target edits. Used in Indian crop biotechnology labs.

22. Machine Learning for Predicting Protein-Protein Interactions

Protocols include SVM-based classifiers trained on protein sequence features. Applied in host-pathogen interaction research.

23. Biosensor Design Using Computational Biology

Protocols involve molecular docking of analytes with sensor surfaces. Used for low-cost biosensor development in India.

24. Metabolomics Data Analysis Using XCMS

Protocols involve peak detection, alignment, and metabolite identification. Applied in Indian nutraceutical studies.

25. In-Silico Vaccine Design Using Reverse Vaccinology

Protocols involve identifying surface antigens, epitope prediction, and immunoinformatics modeling. Applied in India for leptospirosis and tuberculosis vaccines.

26. Comparative Transcriptomics of Stress-Responsive Genes

Protocols involve differential expression analysis across multiple species. Indian labs use this for drought-tolerant crops.

27. Genome Editing Outcome Prediction Tools

Protocols involve analyzing Cas9/Cas12 cut efficiency. Used in Indian gene editing projects.

28. Molecular Docking of Nanoparticle-Drug Conjugates

Protocols involve docking nanoparticles with biological membranes. India uses this in nanomedicine development.

29. Proteome-Wide Analysis of Post-Translational Modifications

Protocols involve prediction of phosphorylation/glycosylation sites using bioinformatics tools. Used in Indian cell signaling research.

30. Big Data Analytics in Genomics

Protocols involve Hadoop/Spark frameworks for large-scale genomic datasets. Indian genome projects generate massive data requiring such tools.

31. Cancer Genomics Using TCGA Data

Protocols involve analyzing mutation, CNV, and expression profiles from TCGA. Applied in India for oral and breast cancer studies.

32. Population Genomics of Indian Human Diversity

Protocols involve SNP genotyping, admixture analysis, and PCA. Indian Genome Variation Consortium applies such studies.

33. Cloud Computing in Bioinformatics

Protocols involve using AWS/GCP platforms for scalable genome analysis. Indian labs increasingly use cloud services.

34. Protein-Protein Docking Using HADDOCK

Protocols involve docking large protein complexes and analyzing interfaces. Applied in vaccine and antibody research.

35. Transcriptome Assembly Using Trinity

Protocols involve de novo assembly of RNA-Seq reads. Indian research applies this for non-model organisms like medicinal plants.

36. Drug Resistance Mutation Prediction

Protocols involve computational modeling of mutations in pathogen proteins. India applies this in TB and malaria research.

37. Next-Generation Data Compression in Genomics

Protocols involve specialized algorithms to compress FASTQ/FASTA files. Crucial for India’s genome databanks.

38. CRISPR Base Editing Prediction Tools

Protocols involve simulating cytosine/adenine base editing outcomes. Cutting-edge field for precision gene editing.

39. AI Models for Disease Outbreak Prediction

Protocols involve machine learning models trained on epidemiological + climate data. Indian bioinformatics teams apply this for vector-borne diseases.

40. Molecular Docking in Antimicrobial Resistance Studies

Protocols involve docking antibiotics with mutated bacterial proteins. Applied in India’s AMR research programs.

41. Multi-Omics Integration for Crop Yield Prediction

Protocols involve merging genomics, transcriptomics, and phenomics datasets. Applied in Indian rice breeding programs.

42. Cryo-EM Data Analysis with Bioinformatics Tools

Protocols involve image processing pipelines for protein structure refinement. Globally important, with growing Indian contributions.

43. Gene Regulatory Network Reconstruction

Protocols involve inferring GRNs using algorithms like ARACNe. Used in plant stress biology studies.

44. Bayesian Models in Evolutionary Genomics

Protocols involve posterior probability estimation of phylogenies. Applied in Indian labs for viral evolution research.

45. AI-Powered Drug-Target Interaction Prediction

Protocols involve deep neural networks predicting binding affinities. Applied in Indian pharma bioinformatics.

46. Exome Sequencing Analysis for Rare Diseases

Protocols involve variant calling, annotation, and prioritization. Applied in India for pediatric genetic disorders.

47. Protein Folding Simulations Using Molecular Dynamics

Protocols involve long-timescale MD to observe folding events. Indian HPC centers enable such simulations.

48. Synthetic Biology Circuit Design Using Computation

Protocols involve Boolean modeling of genetic circuits. Applied in India for microbial engineering.

49. Predictive Toxicology Using In-Silico Tools

Protocols involve docking xenobiotics with human proteins and toxicity prediction. Applied in Indian food safety studies.

50. Blockchain for Genomic Data Security

Protocols involve decentralized encryption of patient genomic data. Emerging globally, with Indian start-ups exploring its use.