* If you downloaded v1.0.2, please update to 1.0.2b, which fixes a bug in the search routine *

pLOT version 1.0.2b is now out.  Aside from a few fixes (listed below) this release includes the automates search for primers in your sequence.  The display of primers on the map can be toggled on and off by clicking on the "Display Primers" button.  Primers are displayed in bold, italicized dark orange font (color customization will be available in upcoming releases).



You can either enter primers one by one or batch enter.  The format for batch entering (described below) is makes it convenient to copy and paste a primer list from an excel table as doing so gives the correct format.

Format: Name <Tab>Sequence<Tab>Comment<Tab>Minimum Anneal Length

• Name: The primer's name.
• Sequence: The primer's sequence entered 5' to 3'.
• Comment: A comment or description of the primer.
• Minimum Anneal Length: The minimum number of matching base pairs (starting at the 3' end and going 5') to be considered a match.  The default is 15 but it can be set higher.  This allows the finding of primer binding sites for primer sequences with 5' restriction sites or modifications not present in the fragment to be amplified.

Example: Batch Primer Addition
1. Click the "Primer Manager" menu item under "Tools" to open up the manager

2. Click the "Batch Add Primers" tab at the top of the screen to swap to batch entry mode

3. Copy the data from an excel sheet or from any properly formatted text file.  These primers sequences were taken from OpenWetWare.org's Common Primer page [1].

4. Paste the table into the text box in the Primer Manager

5. And then click "Add Primers".  This will add the primers and return you to the main manager tab.

6. If you want to undo the additions, you can click cancel to exit or click "Save and Close" to apply the changes you've made and return to the current project.

Download Links
*If you have previously installed v1.0.1 or v1.0.0, you will need uninstall it and run the complete v1.0.2b installation file first.*

pLOT v1.0.2b Update
(v1.0.2b has been replaced by 1.0.3a)


Please feel free to like the pLOT Facebook Page for up-to-date information on new releases, to report bugs, or to suggest new features.

*** Change history ***
v1.0.2b
 - Fixes an error in the search routine that returned antisense matches at the wrong bp.
v1.0.2
 - Text boxes changed to accommodate larger sequences.
 - Other "under the hood" changes and fixes
v1.0.1
 - Addition of gaps in search strings
 - Added Primer Manager
V1.0.0
 - Initial release.

1. http://openwetware.org/wiki/Common_primer_sequences