ApE A plasmid editor

I've started a YouTube channel with tutorial videos. youtube.com/channel/UC_-pO… There are 11 so far in the tutorial playlist. youtube.com/watch?v=HTq91g… Let me know if you have requests for any topics I should add to the tutorials.

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

@idreesashah I have at least a partial fix in v 3.1.9 (just posted recently). Does it still happen in that version?

@ApEplasmid Why does @ApEplasmid hang wil little large sequence. Can it be fixed.?

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

@revgalerivs The toolbar icon size can be set in the preferences. Contol-clicking the toolbar lets you configure the layout. If this isn't available, update to a newer version. The menu bar text font and size are set by the main OS settings.

@ApEplasmid I can not see well menu and tools. like resolution is way too small i tried to change settings and all places I knew, but it is still small

@ApEplasmid why do we see difference in the number of restriction enzymes displayed in two laptops having same version of ApE

@idreesashah The Letter and Number codes next to each enzyme are the Rebase supplier codes and the suggested digestion temperature.

@idreesashah If you do a lot of Golden Gate cloning, you probably want to add your common GG enzymes to your default set to use in the GG tools. Those enzymes are specifically available in the Golden Gate tab of the enzyme selector sub-dialog

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).

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-Primer-Des…

@cajovxus In the latest version, you can annotate primer features that have a mismatch. When you use those in the PCR tool mismatch is incorporated. The only thing left to do is represent the mismatch graphically in the inline mode. email or DM for more info.

@ApEplasmid love your app. Feature request: have primers with mismatch. Now I can just select bases and add as a feature. It would be really cool if it would support mismatches though. Similar to what SnapGene does. It even shows the mismatch as a bulge in the inline arrow

@SPAVINASHX @ATinyGreenCell It's desktop software (MacOS, Windows, Linux) jorgensen.biology.utah.edu/wayned/ape/

@ApEplasmid @ATinyGreenCell Excellent, can you share it? Is it a webtool or software?

@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)

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

You can store reactions that you use a lot and multiply a master mix recipe