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

• Mega works on Windows, Mac OS, and Linux

• You can download the new version Mega 5, or the older versions.

Get the mRNA sequence of chicken LDH-A (accession X53828) from the database

Choose “Query Databanks”

Get the mRNA sequence of chicken LDH-A (accession X53828) from the database

Choose “Query Databanks”

Search for the sequence

Choose “Query Databanks”

Search for the sequence

Add to Alignment

Get the mRNA sequence of chicken LDH-A (accession X53828) from the database

Scroll down and follow the link to the CDS

Now, get only the CDS:

• Scroll down and follow the link to the CDS

• Get the fasta sequence

• Add to Alignment

Now, get only the CDS:

Close the MEGA Web-Browser and examine the mRNA and CDS sequences

Alignment Explorer

Edit the names of the sequences

Alignment Explorer

Edit the names of the sequences

Alignment Explorer

Alignment Explorer

Align the DNA sequences

Alignment Explorer

Can you identify the start site of translation?

Alignment Explorer

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

Alignment Explorer

At the DNA level, cut the UTR region from the mRNA

Alignment Explorer

Align the DNA sequences again and translate to proteins

Alignment Explorer

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

• 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

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

Further analysis

To be continued…