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LABORATORY XI
Course Outcomes (COs):
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Course Outcomes |
Learning and teaching strategies |
Assessment Strategies |
|---|---|---|
|
Upon completion of the course the learner will: CO 121: Describe contents and properties of most important bioinformatics databases CO 122: Perform text- and sequence-based searches and analyze and discuss results in light of molecular biological knowledge CO 123: Explain major steps in pairwise and multiple sequence alignment, explain principle and execute pairwise sequence alignment by dynamic programming CO 124: 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 |
CONTENTS
- Using NCBI and Uniprot web resources.
- Introduction and use of various genome databases.
- Sequence information resource: Using NCBI, EMBL, Genbank, Entrez Swissprot/ TrEMBL, UniProt.
- Similarity searches using tools like BLAST and interpretation of results.
- Multiple sequence alignment using ClustalW.
- Phylogenetic analysis of protein and nucleotide sequences.
- Use of gene prediction methods (GRAIL, Genscan, Glimmer).
- Using RNA structure prediction tools.
- Use of various primer designing and restriction site prediction tools.
- Use of different protein structure prediction databases (PDB, SCOP, CATH).
- Construction and study of protein structures using Deepview/PyMol.
- Homology modelling of proteins.
- Use of tools for mutation and analysis of the energy minimization of protein structures.
- Use of miRNA prediction, designing and target prediction tools.
