Fundamentals of Omics Lab

List of Experiments / Activities

1. 1Retrieve DNA sequences from NCBI and visualize basic sequence features.
2. 2Primer designing.
3. 3Perform gene prediction using AUGUSTUS (web server demo).
4. 4Explore mutation detection using DeepVariant demo dataset.
5. 5Load RNA-Seq sample data in Galaxy and generate expression plots.
6. 6Cluster transcriptomic data using Orange Data Mining (drag-and-drop).
7. 7Retrieve protein sequences from UniProt and analyze domains using InterPro.
8. 8Predict protein secondary structure using SOPMA/PSIPRED online tools.
9. 9Phosphorylation site prediction using NetPhos.
10. 10Peptide structural characterization by Bioinformatics tool.
11. 11Identify motifs in protein sequences using HMMER web server.
12. 12Map genes/proteins to pathways using KEGG Mapper.
13. 13Run a simple neural network in Google Colab to classify DNA vs. protein sequences.
14. 14Apply K-means clustering on demo gene expression data (Orange/Colab).
15. 15Case study: Use Orange’s built-in healthcare dataset to train a decision tree classifier.
16. Note: The instructor may add / delete / modify / tune experiments as required. Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh