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•Automatic and manual sequence alignment
•Inferring phylogenetic trees
•Mining web-based databases
•Estimating rates of molecular evolution
•Testing evolutionary hypotheses
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Mega works on Windows, Mac OS, and Linux
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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
Get the mRNA sequence of chicken LDH-A
(accession X53828) from the database
Choose
“Query Databanks”
Search for the
sequence
Add to Alignment
Now, get only the CDS:
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
Alignment Explorer
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
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
Alignment Explorer
• 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?
Further analysis
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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…