Syllabus
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Course Code: IN-BTY-608 Course Name: Bioinformatics-Practicals |
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| MODULE NO / UNIT | COURSE SYLLABUS CONTENTS OF MODULE | NOTES |
|---|---|---|
| 1 | 1. Types & Examples of Biological Databases (Primary and Secondary), their URLs and Major functions. | |
| 2 | 2. NCBI (PubMed, Nucleotide): Literature search and Data retrieval. (How to do literature search using NCBI’s PubMed & Data retrieval of a gene using NCBI’s Nucleotide database). | |
| 3 | 3. Download Human Haemoglobin gene from NCBI database in GenBank and FASTA format. | |
| 4 | 4. Using NCBI Nucleotide database, search and download FASTA file of a Human gene (e.g. BRCA1), run BLAST at NCBI website. | |
| 5 | 5. Global alignment: Make scoring matrix of these two sequences, ACGGCTC & ATGGCCTC using values as match= +1, mismatch= -3, gap penality= -4. | |
| 6 | 6. How to run BLAST software (Nucleotide BLAST, blastx, tblastn, Protein BLAST) and their uses. | |
| 7 | 7. Run ClustalW for Multiple sequence alignment of three human proteins. | |
| 8 | 8. Phylogenetic tree construction using PHYLIP program. | |
| 9 | 9. Prokaryotic gene finding using GLIMMER, Eukaryotic by GENSCAN program. | |
| 10 | 10. Major steps of Eukaryotic Genome Assembly (Whole Genome Assembly). | |
| 11 | 11. Protein structure prediction by HMM profile (sequence) based method. | |
| 12 | 12. To perform prosite for domain perdiction | |
| 13 | 13. To perform Pfam for motif prediction | |
| 14 | 14. To perform RNA FOLD for rna structure prediction | |
| 15 | 15. To perform jpred | |
| 16 | 16. To perform GENSCAN | |
