1. Automatic and manual sequence alignment Inferring phylogenetic trees Mining web-based databases Estimating rates of molecular evolution Testing evolutionary hypotheses

2. Mega works on Windows, Mac OS, and Linux You can download the new version Mega 5, or the older versions.

3. Get the mRNA sequence of chicken LDH-A (accession X53828) from the database Choose “Query Databanks”

4. Get the mRNA sequence of chicken LDH-A (accession X53828) from the database Choose “Query Databanks” Search for the sequence

5. Choose “Query Databanks” Search for the sequence Add to Alignment Get the mRNA sequence of chicken LDH-A (accession X53828) from the database

6. Scroll down and follow the link to the CDS Now, get only the CDS:

7. Scroll down and follow the link to the CDS Get the fasta sequence Add to Alignment Now, get only the CDS:

8. Close the MEGA Web-Browser and examine the mRNA and CDS sequences Alignment Explorer

9. Edit the names of the sequences Alignment Explorer

10. Edit the names of the sequences Alignment Explorer

11. Align the DNA sequences

12. Alignment Explorer Can you identify the start site of translation?

13. Alignment Explorer Translate the alignment to protein. What’s wrong here?

14. Alignment Explorer At the DNA level, cut the UTR region from the mRNA

15. Alignment Explorer Align the DNA sequences again and translate to proteins

16. Alignment Explorer Create a new alignment, from the FASTA file ldh_a-c.fas

17. You can either (1) align the sequences at the DNA level and then translate to protein sequences, or (2) translate the DNA sequences to protein sequences and then get the alignment. Try both. Which one gives better results? Alignment Explorer

18. Further analysis Export alignment to mega format Save the data to a MEGA file Give it an appropriate title Specify if it is a protein-coding sequences Open the data file in the Sequence Data Explorer

19. Further analysis To be continued…