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UGENE Forum › General Category › Feature Requests › A "cloning" plugin

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A "cloning" plugin (Read 36716 times)

Reply #15 - Jun 21^st, 2010 at 11:23am

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Sebastian, John,
thanks for the suggestions and detailed explanation!

We are planning to improve cloning pipeline in version 1.7.2 ( scheduled for September 2010) and further releases. Stay tuned for UGENE updates.

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Reply #16 - Feb 9^th, 2011 at 1:50pm

Peacemaker Offline
YaBB Newbies

Posts: 12

Thank you very much for fixing the bug I reported a few days ago (http://ugene.unipro.ru/forum/YaBB.pl?num=1296858562) so fast. It' s working fine now. Additionally I have two suggestions for you which would in my opinion simplify the working with the cloning pipeline.
1. Since the widely used expression vectors of the pET system (Novagen, http://www.emdchemicals.com/life-science-research/pet/c_2tOb.s1OkacAAAEjWhl9.zLX) are numbered by the pBR322 convention (the T7 expression region is reversed on the
circular map) it would be nice to be able to reverse complement a fragment during cloning (without first creating a new molecule in Ugene). Maybe you could add an option like "Reverse complement Fragment" or "Invert fragment" in the "Edit molecule fragment" dialog of the cloning pipeline.
2. Since you are sometimes cloning PCR fragments into a blunt end cutted vector, it may be useful to be able to add DNA molecules from the current Ugene project into the cloning pipeline. Maybe you could add an option like "Add molecule from current project" to the "construct molecule" dialog. Due to clarity, I would not suggest to add all molecules to the "Available fragments" selection by default.
Thank you again for Ugene.
Best regards

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Reply #17 - Feb 9^th, 2011 at 5:17pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

These two suggestions are interesting features indeed, especially the second one: adding molecule from project and refering to it as a fragment. I suppose nice implementation will be a "fragment manager" - container of fragments for active project with possible options to create new fragments: import documents from project, PCR amplication, etc.
However the first implementation most likely will be, as you suggested, option for import project documents in "Construct Molecule" dialog.

We will put these features on our TODO list for 1.9.2.

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Reply #18 - Feb 25^th, 2011 at 5:42pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Peacemaker wrote on Feb 9^th, 2011 at 1:50pm:

... Additionally I have two suggestions for you which would in my opinion simplify the working with the cloning pipeline.
1. Since the widely used expression vectors of the pET system (Novagen, http://www.emdchemicals.com/life-science-research/pet/c_2tOb.s1OkacAAAEjWhl9.zLX) are numbered by the pBR322 convention (the T7 expression region is reversed on the
circular map) it would be nice to be able to reverse complement a fragment during cloning (without first creating a new molecule in Ugene). Maybe you could add an option like "Reverse complement Fragment" or "Invert fragment" in the "Edit molecule fragment" dialog of the cloning pipeline.
2. Since you are sometimes cloning PCR fragments into a blunt end cutted vector, it may be useful to be able to add DNA molecules from the current Ugene project into the cloning pipeline. Maybe you could add an option like "Add molecule from current project" to the "construct molecule" dialog. Due to clarity, I would not suggest to add all molecules to the "Available fragments" selection by default.

Good news! The suggested features are implemented and available via latest snapshot. Check attached screenshot for quick help.

cloning_in_silico_new_features.gif (21 KB | )

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