[Arabidopsis] Vector NTI Replacement Replies

Holt, Ben F. III via arab-gen%40net.bio.net (by benholt from ou.edu)
Tue Dec 1 12:03:08 EST 2009


Hi Everyone,

Below I have pasted all the comments I got regarding the Vector NTI Replace=
ment question. There are a variety of solutions suggested and a few seem to=
 be favored by a number of groups =96 ApE Plasmid Editor is a crowd favorit=
e, but there are a lot of suggestions to consider, so have at it!

As a side note, I would like to say that we are extremely fortunate to have=
 developed this type of research community around the Arabidopsis model sys=
tem. We should be thankful for the many researchers who laid the groundwork=
 for this community and continue to do our part to maintain this level of c=
ross-border camaraderie.

Good luck in your research endeavors,
Ben Holt

=3D=3D=3D=3D=3D=3D=3D=3D
Ben Holt
Assistant Professor
University of Oklahoma
Department of Botany and Microbiology
GLCH Rm 219
770 Van Vleet Oval
Norman, OK? 73019
Phone (405)325-9018
FAX?? (405)325-7619
http://www.ou.edu/cas/botany-micro/faculty/holt.html



I have used ApE Plasmid Editor. Its not as slick as Vector NTI but if
you have not seen it then it could be worth a look. Here is the link:

http://www.biology.utah.edu/jorgensen/wayned/ape/

Vid
PhD - Research Assistant, Molecular Biology,
Wageningen University,
The Netherlands.
___________________________________________________________

Where using Geneious from Biomatters and we're extremely happy with it.
It's not too expensive and there is a lot of potential add-on for free.
There is a free basic version to try.

Ghislain Breton (Kay lab)
___________________________________________________________

We use ApE (http://www.biology.utah.edu/jorgensen/wayned/ape/) for
working with vector sequences. It's easy to use, free and can simulate
the gateway recombination reactions. I also use OligoChecker
(http://www.ahatfullofsky.comuv.com/English/Programs/OligoChecker/OligoChec=
ker.html)
to keep track of oligos. What I miss, which vector NTI had, is a way to
assemble contigs from sequencing reads. I haven't found any good free
alternatives for this.
Hope this helps - if you hear of anything better let me know.
Richard
___________________________________________________________

For building plasmid maps, planning cloning experiments and restriction
enzyme digestions, we use pDRAW32 (http://www.acaclone.com/). For the
purposes described, it works quite well, and best of all its free.

pDRAW32 clearly doesn't have the many features/capabilities of VectorNTI
or some other programs, but it is free, and is relatively easy to learn
and use.

For the alignment and analysis of raw sequence data we use an ancient
version of DNAStar (SeqMan, EditSeq etc). For other sequence
manipulations we need to perform, we use various tools freely available
on the web.

Regards,
Roger

Roger Thilmony, Ph.D.
Crop Improvement and Utilization Research Unit
Western Regional Research Center
USDA-Agriculture Research Service
800 Buchanan Street
Albany, CA 94710-1105
___________________________________________________________

Thanks for initiating this topic. Serial Cloner is a good freeware choice, =
but has limited capabilities compared to vector NTI for data management. I =
am currently considering Lasergene (from DNA star) which has perpetual lice=
nse unlike vNTI, but is not free/inexpensive.

Please let me know what you hear from others.

Regards,
Sen

Senthil Subramanian,
Assistant Professor,
Plant Science Department,
Office: NPB245D, Lab: NPB137
South Dakota State University,
Brookings, SD, 57007
___________________________________________________________

Some people advised the STADEN package
http://sourceforge.net/projects/staden/files/ since its free, and is
available for linux, windows or mac. It still requires fair a bit of
detailed computer knowledge to install and so I don't find it user
friendly and am still looking for something.

Josh

----
Dr Joshua S. Mylne
ARC QEII Fellow

Institute for Molecular Bioscience
The University of Queensland
St Lucia, QLD, 4072
AUSTRALIA
___________________________________________________________

I'd be curious to know what you find out about this -- could you post
a compilation of answers?

For us, we use DNA Star Software to deal with sequences, but it really
doesn't do what VectorNTI does.  However, we can't afford VectorNTI.

Thank you,

Raka
___________________________________________________________

I am in the same situation. Vector NTIs annual fee is far to high for me to=
 afford ...

So far, I have been looking at Redasoft Visual Cloning 2000 and PremierBios=
oft SimVector.

I found Visual Cloning (www.redasoft.com) pretty easy to use and very intui=
tuve. But, I also found it not as convenient as Vector NTI for cloning. For=
 instance, for fast checking of sequences in certain areas, highlighting a =
gene or fragment in the graphic map does not show you the according sequenc=
e in the sequence window. The cost is more reasonable than NTI. It's a US$ =
9.95 month-to-month subscripion for academic institutions. I inquired about=
 a one time payment instead (our accounting department has problems with "l=
easings") - it's available at US$595.

SimVector (www.premierbiosoft.com) seems much more near to Vector NTI in fu=
nctions and handling. I played around with the demo and it basically fits m=
y need. The cost is US$ 685 (list) to 485 (insitutional).

I did not try any other software, yet. So far, I am leaning towards SimVect=
or but I didn't really decide yet. Please, let us know if you get any other=
 suggestions.

Regards,
Klaus

----------------------------------------------------------
Dr. Klaus Eimert
Dept. of Botany
Geisenheim Research Center
Von-Lade-Str. 1
D-65366 Geisenheim
Germany
___________________________________________________________

It's not nearly the same level of power, but prior to Vector NTI, I was usi=
ng pDRAW32.  I went back to it.
pDRAW32 is "beerware" and license-free.


http://www.acaclone.com/ <http://www.acaclone.com/>


David Bird
Chemical and Biological Sciences
Mount Royal University
4825 Mount Royal Gate S.W.
Calgary, AB  T3E 6K6
Ph:  403- 440-8750
Fx:  403-440-6095
=AD___________________________________________________________

We were fans of VectorNTi as well, our institute (140 people) has now
bought Clone Manager from scied, it does the job, for quite a cheaper
price.

Nemo

Nemo PEETERS,
PhD, CR1 INRA

LIPM, UMR CNRS-INRA 2594/441
BP52627 31320 Castanet Tolosan
France







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