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The Swiss Institute for Bioinformatics provides a JAVA applet that perform interactive dot plots. Since September 2015 the chome browser does not support JAVA applications. You will need to run today's exercises in Safary or Firefox. The application is called Dotlet (if site doesn't load, try here, here, here, or here). You will need to set the JAVA security setting to allow a particular site to run a script; see here for instructions. Under MacOSX, you also might need to go to the general security settings in system preferences and click on the "open anyhow" button. The main use of dot plots is to detect domains, duplications, insertions, deletions, and, if you work at the DNA level, inversions. (Note dotlet compares to both strands, and if you compare DNA and protein, the DNA is "translated" in the three forward reading frames. Excellent illustrations of the use of dot plots are given on the examples page).
Jalview is a JAVA application to inspect and edit multiple sequence alignments. It also allows inspection of protein space for the aligned sequences.
This works surprisingly well.
The Jalview Homepage contains a lot of additional information and links to install the Jalview desktop on your computer (especially recommended for Macs).
Go to the jalview applet page and - after page has finished loading and you ganted hte necessary permissions - either start the Jalview desktop (link on top), or a jalview applet (links in the middle of page).
If this does not work, download the Jalview desktop from the Jalview Homepage (follow instructions), or on the old macs in computerlab, download this file, unarchive it, and double-click on Jalview.app.
Preferably, you want to load the JaLVIEWdesktop, but the Jalview lite version is just as fine, except the sequence input is more difficult (delete the sequences from the example, add the sequences form the file).
Close the windows that may have opened as a demonstration, except for the multiple sequence alignment window.
Load the sequences from the ATP-ase Subunit alignment into Jalview (either load from file, if the desktop application runs, or paste into the input window -- select new window after you are done pasting.).
Explore the different coloring options (COLOUR menu). Which one seems to work best (most meaningful - scroll through the alignment to a more conserved region).
Note: You can change/edit the alignment
by clicking on an amino acid residue and dragging it to the right or left using the arrow keys. Try it, but leave the sequences in an aligned state before you move on. (If this doesn't work, presss F2 and try again)
Select all sequences. CALCULATE an AVERAGE DISTANCE TREE USING % identity
Click somewhere in the resulting tree to color groups of related sequences in the same color. You can right-click (or command click) on a node to change color for a group of sequences.
Chose a color scheme that colors all subunits of the same type in the same color
CALCULATE the PRINCIPAL COMPONENT ANALYSIS.
In a principal component analyses, the new dimensions are calculated as a linear combination of the original dimensions, so that greatest variance by any projection of the data set comes to lie on the first axis, etc. for the following dimensions. Can you find a higher dimension that breaks up the vacuolar ATPase A subunits? (Their names start with A.).
Which of the A subunit sequences cluster together, if you use this dimension (1, 2 and 4 worked for me)?
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