Automatic and manual sequence alignment Inferring phylogenetic trees Mining web-based databases
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Transcript of Automatic and manual sequence alignment Inferring phylogenetic trees Mining web-based databases
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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
• You can download the new version Mega 5, or the older versions.
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Get the mRNA sequence of chicken LDH-A (accession X53828) from the database
Choose “Query Databanks”
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Get the mRNA sequence of chicken LDH-A (accession X53828) from the database
Choose “Query Databanks”
Search for the sequence
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Choose “Query Databanks”
Search for the sequence
Add to Alignment
Get the mRNA sequence of chicken LDH-A (accession X53828) from the database
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Scroll down and follow the link to the CDS
Now, get only the CDS:
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• Scroll down and follow the link to the CDS
• Get the fasta sequence
• Add to Alignment
Now, get only the CDS:
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Close the MEGA Web-Browser and examine the mRNA and CDS sequences
Alignment Explorer
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Edit the names of the sequences
Alignment Explorer
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Edit the names of the sequences
Alignment Explorer
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Alignment Explorer
Align the DNA sequences
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Alignment Explorer
Can you identify the start site of translation?
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Alignment Explorer
Translate the alignment to protein. What’s wrong here?
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Alignment Explorer
At the DNA level, cut the UTR region from the mRNA
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Alignment Explorer
Align the DNA sequences again and translate to proteins
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Alignment Explorer
Create a new alignment, from the FASTA file ldh_a-c.fas
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• 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
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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
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Further analysis
To be continued…