Hi all,
Bearing in mind the original post's account of being screwed by the originally-free-of-charge VectorNTI, I strongly recommend rejecting software that isn't free-as-in-freedom. Particularly ones using nonstandard formats or which store your data 'in the cloud', meaning they can be taken from you at any time, or spied upon, or simply are difficult to transfer elsewhere with annotations intact.
GENtle 1/2 (which seemingly bear no relation) are good bets. The former is old, unmaintained, and unstable, but quite feature-rich. The latter is a newer webapp, it's true, but it's either Open Source or Free Software (Can't recall), meaning you can host your own for you and your friends and keep your autonomy.
Personally I no longer find these (vector programs) very useful for engineering, preferring a scripted approach, but I'll grant you options in this regard are very limited right now. I'll happily castigate even my own attempt, fastac, as being truly dishusting, but that's what happens when you splice Multi-FASTA with bash scripting..
Benchling (https://benchling.com) is free, pure HTML5 app so there's no installation required. You can check out the demo directly here. We posted about it just a bit earlier on the DIYBio mailing list. It'll support your plasmid editing needs, as well as sangar sequence trace viewing, basic sequence alignment, primer searching, etc.
Best thing is that it's all online, so you can share sequences with friends and colleagues just via links.
On Saturday, September 28, 2013 8:43:46 PM UTC-7, Dunqiang Liao wrote:VectorFriends, free for academic researchers. It combines various types of cloning simulations, sequence analysis and data management into one application.http://www.vectorfriends.com
On Sunday, February 14, 2010 2:18:47 AM UTC+8, Mackenzie Cowell wrote:APE - a plasmid editorhttp://www.biology.utah.edu/jorgensen/wayned/ape/ Clotho - iGEM project partially by APE, but with additional features for engineering biobricks.EnzymeX from MekenTosjI personally recommend clotho: http://vimeo.com/2218118 Cheers,MacOn Sat, Feb 13, 2010 at 12:43 PM, Marshall Louis Reaves <marshal...@gmail.com> wrote:
So, Invitrogen did this rather sleazy thing where they got everyone
using VectorNTI because it was free for a long time, and now its not
free, even for academic users.
Does anyone know about any reliable freeware for organizing and
analyzing plasmid sequence data?
Thanks!
MLR
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