automated annotation of features

[Joemoe134]

Hello, thanks for this great tool. I have been using a lot of different vector editors, but am very pleased with OVE. Is there a way to annotate sequences based on sequence matches from a library? I would love to annotate new vectors automatically with basic info such as antibiotic resistance, promoters and standard primer binding sites.

Cheers Jochen

[tnrich]

Hey @Joemoe134 , glad you're liking OVE-electron :)

That functionality exists in the app my company works on (teselagen.com), but not yet as a standalone feature of ove-electron. I could imagine adding a simple tool to do auto-annotation to this repo sometime in the future but it isn't currently a high priority for me. Of course I'd be happy to accept a PR adding it.

Cheers, Thomas

[IbanezP]

hi please find attached a few screenshots of a great software that does it (Ape https://jorgensen.biology.utah.edu/wayned/ape/) in two flavors : "features" that are within the sequence file, or "feature library" that are features that can be recorder in a library (text file with Name, sequence, tyoe of sequence, forward colour, reverse colour tab separated that can be called from the menu) and used to automatically annotate any new sequence. If something close to that could be achieved, that would be extremely useful. Thanks ApeFeatures.pdf

[tnrich]

@IbanezP @Joemoe134 I'm starting to develop a simple auto annotate addon specifically for OVE electron. Would it be enough to have it read in an ApE feature library file and use that to auto annotate? Does it also need to have the ability to edit that file or add to it?

Just wondering what I can get away with as a first pass. Obviously the functionality within our main teselagen app is much more fully fledged (with editable annotation groups and the like). I just don't yet have the time to make that happen for ove-electron.

Thanks! Thomas

[IbanezP]

Hi Thomas and thanks for all your efforts! For me, the simplest annotation addon would do, ie even a .csv kind of file that could identify the sequences of interest, highlight it ans name it would be more than enough. Adding and editing could be done directly in the .csv file : it might actually be easier in cases like primers that can already be in a .csv/.ods/.xcl for bulk ordering, or for constricts that can be designed using concatenation : in fact, that could be the entrance door to some kind of dna construct design tool (golden gate assembly, gibson, restriction ligation, pcr, ...) that would generate a dna map at the end of the process (my dream). Could you please send me a link to your teselagen app so that I can have a look? I hope it helps Thanks Pablo

Le ven. 21 mai 2021 à 20:07, Thomas Rich @.***> a écrit :

@IbanezP https://github.com/IbanezP @Joemoe134 https://github.com/Joemoe134 I'm starting to develop a simple auto annotate addon specifically for OVE electron. Would it be enough to have it read in an ApE feature library file and use that to auto annotate? Does it also need to have the ability to edit that file or add to it?

Just wondering what I can get away with as a first pass. Obviously the functionality within our main teselagen app is much more fully fledged (with editable annotation groups and the like). I just don't yet have the time to make that happen for ove-electron.

Thanks! Thomas

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tnrich/ove-electron/issues/17#issuecomment-846142647, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEVJV7OPVHQGC4RL6K6RLZLTO2OPDANCNFSM4XKRWOPQ .

--

-- Pablo M. IBÁÑEZ CRUCEYRA, PhD Postdoctoral Researcher

Andrew D. GRIFFITHS Lab

---

+--------------------------+ | ESPCI ParisTech | +==========================+ | Laboratoire de Biochimie | +--------------------------+ bâtiment B 2ème étage porte B229 +------------------+ | 10 rue Vauquelin | +==================+ | 75005 Paris | +------------------+ | France | +------------------+

Office: +33 (0) 1 40 79 45 87NEW Mobile: +33 (0) 7 78 70 57 17Email: @.***NEW Jitsi: https://meet.jit.si/PabloIbanezCruceyra________

École supérieure de physique et de chimie industrielles de la Ville de Paris 10, rue Vauquelin | 75231 Paris Cedex 05 | France

• 33 1 40 79 44 00https://www.espci.psl.eu/en/

[tnrich]

@IbanezP cool thanks for the response! I'll let you know when the feature is released.

In the meantime, maybe @mfero and @ccwilson can get you hooked up with a new "Academic Edition" of our full fledged app.

[tnrich]

Hey @IbanezP this should soon exist as a feature in ove-electron. It will look like so:

You can try it out already at http://teselagen.github.io/openVectorEditor/#/Editor

[tnrich]

@IbanezP here's the latest release: https://github.com/tnrich/ove-electron/releases/tag/v1.2.1