pLOT 1.0.11c allows for pattern searching for prokaryotic promoter-like sequences as well as Shine-Dalgarno- and Kozak-like sequences.  The searched sequences can be added as features from the window and their associated ORFs can be optionally annotated as well.

For Kozak and Shine Dalgarno searches, clicking on any of the found items in the list box shows the amino acid sequence of the associated ORF in the lower text window.  After a search has been made, you can filter by entering the ORF size limit and >, <, = followed by clicking "Filter ORFs"

The search window can be accessed through the Tools>Promoter Element Search menu.

In the figure below, the pX330 vector was searched for Kozak signals in the sense direction only using a cutoff of 0.8.  The top score is the signal associated with the Cas9 ORF.  Clicking the Green "+" adds the selected Kozak signals as annotations.  Clicking the blue "+" adds the selected Kozak signals and their ORFs as annotations.

pLOT 1.0.11c Download Links

pLOT v1.0.11c 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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