Pick a sequence alignment from the table below:
| ppck.fasta | gprot.fasta | cryst.fasta |
| clamp.fasta | cytcox.fasta | thrRS2.fasta |
Perform a Multiple Sequence Alignment using the CLUSTALW web server. Be sure to look at the help page first. This is a requirement for our use of the server for class.
Paste your sequences into the sequence box at the bottom of the page. Try both the Full (slow) and Fast algorithms and compare your results. Email both the .aln and .dnd files to me. Alternatively, you could compare results for one of the CLUSTAL programs with results using Multalin.
How many identical residues did you find in your alignment (*)? How many highly conserved (:)? How many moderately conserved (.)?
Did you see much difference in the gaps using the other algorithm?
You can try editing the alignment by sliding the letters. If you like your
alignment better, send that too. Jalview also will display tree diagrams from
the clustal .dnd files. Got to the "Calculate" menu (Jalview adds
extra menus to the browser menus; look at the right-hand side)
Select "Neighbor Joining tree using PID" (percent identity). the tree
should appear. You can change the font, if you like. You can try having it email
you a postscript file of the tree. I made several attempts, but was unsuccessful.
It might work with your browser, it might not. If you try it,
Click the Output button,
Enter your email. in the new window. Click Apply, wait a minute (your might
see an hourglass prompt), then press close.
If you get a postscript file, you can email it to me an I will make a pdf.
You can get protein distances using the phylip
web interface. Click on the Protdist
page and paste in thetext alignment from the clustalw page (the .aln file).
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Some of you had trouble copying and pasting the ".aln" files and getting no result from the protdist page. If so, try using these prealigned files in a different format instead - the phylip format ".phy:
| ppck.phy | gprot.phy | cryst.phy |
| clamp.phy | cytcox.phy | thrRS2.phy |
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Once you have received a distance matrix result, you will be given the option of building a tree using the bionj neighbor joining method. submit the bionj request and you will receive a treefile result, again you have the option to go on and submit a drawtree request to see your tree. Choose a convenient format, if you choos X bitmap, you may be able to see it in your browser. Otherwise choose postcript or pict and you can email it to me.