分子演化 Molecular Evolution

Homework:

生物多樣性與生態 Biodiversity and Ecology

計算生物實驗 Computational Biology Lab.

Homework:

1. Retrieve the protein sequences of human hemoglobin (alpha 1) and hemoglobin (beta) from database
2. Align these two sequences manually
3. Build a dot matrix for these two sequences
4. Using dynamic programming to align these two sequences
5. Using BLOSUM 62; Compare the obtained result with the previous one and make some discussion
6. Using local alignment; Compare the obtained result with the previous one and make some discussion
7. Using two types of gap penalty; Compare the obtained result with the previous one and make some discussion
8. Align the protein sequences of human hemoglobin (alpha 1) and hemoglobin (zeta). To generate the alignment represented in our textbook, what range of the gap penalty should be assigned?
9. Retrieve all the protein sequences of human and mouse (Mus musculus) hemoglobin from database, and align them based on the alignment result of hemoglobin (alpha 1) and hemoglobin (beta)
10. Calculate pairwise distances
11. Based on the calculated pairwise distances, construct a phylogenetic tree; Make some discussion
12. Retrieve the DNA coding sequences and their corresponding intron sequences of all human hemoglobins, and human TBPL1 (TATA-box binding protein like 1 gene) from the database
13. Calculate GC content for the coding sequences and intron sequences (GCi)
14. Calculate GC1, GC2, and GC3 for the coding sequences
15. Compare GC3 and GCi among these genes
16. Calculate codon usage frequencies for the coding sequences
17. Calculate RSCU values for the coding sequences
18. Retrieve the DNA coding sequences of the virus RaTG13 and Human betaherpesvirus 5 strain SOMA from the database
19. Calculate their GC1, GC2, GC3, and RSCU values
20. Compare the GC1, GC2, GC3, and RSCU values between the two viruses and human genes