Course Details
Subject {L-T-P / C} : LS4291 : Bioinformatics Laboratory { 0-0-3 / 2}
Subject Nature : Practical
Coordinator : Prof. Bibekanand Mallick
Syllabus
1. Visualising and understanding biological data formats, such as GenBank flat file, gen pet, FASTA, nexus, pdb etc.
2. Exploring nucleotide and protein databases: GenBank, EMBL, DDBJ, PIR-PSD, SwissProt, TrEMBL/UniProt.
3. Protein Databank (PDB).
4. Interpretation of different biological data and use of tools of NCBI.
5. Visualising and understanding the 3D structure of macromolecules by molecular viewers: RasMol, Cn3D, Swiss-PDB Viewer.
6. Sequence comparisons & alignment (pair-wise and multiple sequence alignment).
7. Protein secondary structure and prediction using available freeware.
8. Comparative genomics and gene prediction.
9. Prediction of the tertiary structure of proteins by homology modelling.
Course Objectives
- The course will be complementary to LS4201 Bioinformatics theory.
- It’ll help the students to learn how to analyze the sequences and structures of genes and proteins by using bioinformatics approaches.
Course Outcomes
CO 1: Students will have hands-on exposure to use modern bioinformatics tools and resources of biological data for different purposes, such as predicting genes from a stretch of unknown nucleotide sequences, designing primers for PCR, molecular docking to predict a potential drug for a disease, and identifying gene/RNA signatures as possible biomarkers for a disease by analyzing microarray data, etc. <br />CO 2: Students will be self-sufficient and motivated to use tools and databases of bioinformatics to understand biological systems and processes.
Essential Reading
- Michael Agostino, Practical Bioinformatics, Garland Science, 2012, ISBN 9780815344568
- Andreas D. Baxevanis, B. F. Francis Ouellette, Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition, Wiley-Interscience 2 edition (April 6, 2001) ISBN-13: 978-0471383918
Supplementary Reading
- Bujnicki, Janusz M. (Ed.), Practical Bioinformatics, Springer-Verlag Berlin Heidelberg, ISBN 978-3-540-20613-2
- Shui Qing Ye (Eds.), Bioinformatics: A Practical Approach, Chapman and Hall/CRC , ISBN 9780367388751