Monday, May 23, 2016

  pLOT 1.0.11b adds a few more fixes as well as a early stage bacterial promoter search tool.  The tool can be found under the Tools menu.  Clicking on an annotated feature prior to opening the tool window will set the search region to the region of the annotated sequence.  You can change it manually in the window.
The current recommended setting is a threshold of 0.8.  The tool is based on weight matrices from the publication "Redefining Escherichia coli σ70 Promoter Elements: −15 Motif as a Complement of the −10 Motif" by Marko Djordjevic.  The current search does not take the proposed -15 element into consideration but may in the future.  Once a search is completed, found promoters can be added as annotations.  A right click on the window allows for different selection/deselection options.  Finally, the predicted -35 and -10 boxes for each predicted promoter is shown in uppercase in the output and the spacer is shown in lowercase.

The promoter search tool window for pBR322

pLOT 1.0.11a Download Links
pLOT v1.0.11a patch file [Link]

If this is the first time you're installing pLOT, use 
this first 1.0.10j full installation [Link]

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