@ApEplasmid

Multiplatform DNA editing software

 Salt Lake City, UT
jorgensen.biology.utah.edu/wayned/ape/
Joined August 2020
  • Tweets221
  • Following1.8K
  • Followers2.5K
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I've started a YouTube channel with tutorial videos. youtube.com/channel/UC_-pObW… There are 11 so far in the tutorial playlist. youtube.com/watch?v=HTq91gJD… Let me know if you have requests for any topics I should add to the tutorials.

ApE- A plasmid Editor

youtube.com
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Bug fix update to version 3.1.10.1 is live on the site. The Golden Gate dialog is working better now. Let me know if you have any other bugs or other problems.
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Just posted version 3.1.10. Updates to the Golden Gate Assembler- new buttons available in the enzymes dropdown.
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There's a new user manual for ApE
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Available as a pdf from the main site:jorgensen.biology.utah.edu/w…
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Yes, it's missing chapter 18- that's in the works ("Other tools"), but I wanted to get it out sooner than it would take to write that last chapter. Most of those tools are not that interesting to most people.
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Are people seeing a speed up for the inline display in the new version? Is it fixed, not any different, or better but still needs some work? Thanks
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I just uploaded thatlatest version- 3.1.9. This should fix a long-standing problem with slow updates to window size and feature edits when viewing in inline mode. Tested on Mac more than Windows. Let me know if you see any bugs
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ApE A plasmid editor retweeted
Idrees A Shah@idreesashah21 Aug 2025
Replying to @ApEplasmid
@ApEplasmid why do we see difference in the number of restriction enzymes displayed in two laptops having same version of ApE
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Just posted the 3.1.8 update. Let me know if you find any bugs. It opens in inline feature mode. If you prefer compact mode or if you are opening large sequence files, you can turn off inline mode in Preferences (aka Settings).
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Here's a tutorial I wrote on how I design detection and cloning primers using Primer3. Hopefully it's helpful for students. 💚 binomicalabs.notion.site/PCR…

PCR Primer Design | Notion

Prerequisite Protocols

binomicalabs.notion.site
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Replying to @ATinyGreenCell
@ATinyGreenCell The molecular calculator has several tools for simple molecular tasks: You can look up molecular weights (using pubchem.ncbi.nlm.nih.gov, so an internet connection required)
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You can store reactions that you use a lot and multiply a master mix recipe
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The one I use most is the molar reaction calculator- DNA assembly reactions can be more efficient if you have a consistent molar ratio of input fragments. If you have the size of the fragment and your concentrations, you can calculate the volumes of each DNA solution required
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Here's my first attempt at a web pages documentation. This one is for the Golden Gate Assembler tool. Let me know what you think. jorgensen.biology.utah.edu/w…
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I've uploaded new versions of ApE 3.1.7. The Mac version didn't have the correct version number in the "Get Info" window. The Windows and Linux versions had a small bug that prevented them from running. All three errors should now be fixed.
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I just uploaded version 3.1.7. This update fixes a bug that caused failure to recognize some substrates in the Recombination reaction tool. Also the first full version with the option of inline feature display (option in the preferences).
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I'm updating the user interface of ApE. Features and enzyme sites are inline with the sequence. If you can give it a try and email me all the bugs you find, that will help me get this out into wide release.
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New bug fixes, including BBEdit fix. Also a Linux version jorgensen.biology.utah.edu/w… jorgensen.biology.utah.edu/w… jorgensen.biology.utah.edu/w…
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New bug fixes for theme save, Molecular reaction calculator. jorgensen.biology.utah.edu/w… jorgensen.biology.utah.edu/w… jorgensen.biology.utah.edu/w…
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