You can fine-tune the alignment using the arrows. If you click on the dot plot panel, the alignment window at the bottom aligns the two sequences accordingly. Either you can use the levers on top and at the left side to move the display window down and/or to the right, or you can select a compression using the pull-down menu labeled as 1:1 (1:3 or 1:4 usually work) Note: the sequences may be longer than fit into the display window. (I like black for matches, white for mismatches better than the default). The sliding bars below and above the histogram let you select the colors with which matches are depicted. On the right you see a histogram that describes how often window pairs with the indicated score occurred.
#Waterfox java windows#
The program will compare every window of the chosen size in one sequence to all the possible windows in the other sequence. Select a window size between 9 and 15 and click "compute".
Select Neurospora A-subunit ( vma1Neurospora.fa) and the yeast subunit with intein ( Sce_VMA.fa). Yeast_vma1, YeastHO, Neurospora_vma1, Yeast_intein) Give the sequences a name that allows you to recognize which sequence is which (e.g. , once you leave the webpage, the back arrow will only return you to the applet, but you have to input the sequences again (so make sure that your applet is in a separate browser window).Īlso, when you input sequences make sure you Vma1Neurospora.fa (the vacuolar ATPase catalytic subunit from Neurospora crassa) and SceHO.fa (the mating type switching HO endonuclease from yeast), Sce_VMA.fa (the vacuolar ATPase catalytic subunit from yeast), Go to the applet and input the sequences: we do not need to worry about E value cutoffs and low complexity filters. However in this case, we plot all pairwise comparisons between windows, i.e. This is similar to the analysis we did using pairwise blast. (Note dotlet compares both strands, and if you compare DNA and protein, the DNA is "translated" in the three forward reading frames.Įxcellent illustrations of the use of dot plots are given on theĬomparing yeast ATPase catalytic subunit with yeast HO endonuclease. The main use of dot plots is to detect domains, duplications, insertions, deletions, and, if you work at the DNA level, inversions. This version works fine for protein to protein comparisons, but fails tor DNA to protein (exercise 3 below - i.e try to get the applet version to work!). To make these particular JAVA applets dotlet and jalview) run in your browser, you need to find the java sequity panel and add the following exceptions:Ī java script version of dotlet is in beta testing. (Waterfox also works, if you are on a Mac). 
Therefore, you will need to run today's exercises in Warning: Google's Chrome, Safari, firefox, The Swiss Institute for Bioinformatics provides a
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