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LABORATORY XI
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Course Outcomes |
Learning and teaching strategies |
Assessment Strategies |
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Upon completion of the course the learner will: CO121: Describe contents and properties of most important bioinformatics databases CO122: Perform text- and sequence-based searches and analyze and discuss results in light of molecular biological knowledge CO123: Explain major steps in pairwise and multiple sequence alignment, explain principle and execute pairwise sequence alignment by dynamic programming CO124:Predict secondary and tertiary structures of protein sequences |
Discussion, Tutorials, Demonstration, Effective questions, Simulation, Giving tasks, Practical
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Class test, Semester end examinations, Quiz, Solving problems in tutorials, Assignments, Presentation, Individual and group projects |
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1. Using NCBI and Uniprot web resources.
2. Introduction and use of various genome databases.
3. Sequence information resource: Using NCBI, EMBL, Genbank, Entrez Swissprot/ TrEMBL, UniProt.
4. Similarity searches using tools like BLAST and interpretation of results.
5. Multiple sequence alignment using ClustalW.
6. Phylogenetic analysis of protein and nucleotide sequences.
7. Use of gene prediction methods (GRAIL, Genscan, Glimmer).
8. Using RNA structure prediction tools.
9. Use of various primer designing and restriction site prediction tools.
10. Use of different protein structure prediction databases (PDB, SCOP, CATH).
11. Construction and study of protein structures using Deepview/PyMol.
12. Homology modelling of proteins.
13. Use of tools for mutation and analysis of the energy minimization of protein structures.
14. Use of miRNA prediction, designing and target prediction tools.
