Molecular cloning has undeniably changed the trajectory of life-science research. However, without coincident advances in technology and software design, we’d sit, eyes numb, in darkened labs pouring over the As, Gs, Ts, and Cs, to find the patterns we’re looking for.
In the 1990s Vector NTI entered the scene and quickly became the gold standard of plasmid analysis, liberating researchers from the dark ages, giving us the tools to quickly create constructs for our experiments. But every rose has its thorn, and as we all know, after years of being celebrated as the best plasmid analysis package you could buy, it sold out to Invitrogen. Applying the Netflix model (before the Neflix model existed) they proceeded to ramp up prices, angering researchers throughout the world.
Fortunately, there were some folks who took up the plasmid analysis cause, creating some truly outstanding tools, and adhering to the Quartzy model of “researchers fly free”. Here I’ve reviewed a few of the currently available plasmid analysis freeware programs you can download to your Mac or PC.
DNA Strider
Very Basic. Doesn’t appear to have been updated in a long time.
ApE – Mac / Windows
Created by M. Wayne Davis out of The University of Utah, this program may look small but it’s extremely powerful. You can easily upload many file formats including genbank, EMBL, FASTA, and DNA Strider. It can also read ABI sequencing files. In addition, ApE makes creating printable plasmid maps, and restriction digests quite easy. The user interface could use a little touching up, but in general this is an extremely powerful tool that can definitely supercharge your research. Another important fact that I appreciate is that Dr. Davis keeps an active Wiki about the software where he solicits feedback from scientists and responds to it.
PlasmaDNA – Mac / Windows
Created by Alexandre Angers-Loustau, from the University of Helsinki. If you’d prefer a Finnish take on plasmid analysis, there’s PlasmaDNA. This product definitely gets high marks for how it looks, creating beautiful plasmid maps with little effort. The Digested fragments are also easily displayed either on a virtual gel or in picture form. I had difficulty navigating the “Cloning” window, and eventually gave up. I also found importing FASTA files difficult. Bottom line is that this is a great basic plasmid editor that creates pretty maps.
Serial Cloner 2.1 –Mac / Windows
A pretty amazing suite of plasmid analysis package from Franck Perez, a cancer researcher at the Institute Curie in Paris. It does a great job of combining an intuitive graphic interface with powerful features. Of the tools reviewed in this post, this one comes the closest to giving you the power and usability that VectorNTI does (except that unlike VectorNTI it is free). You can easily import, translate, and create restriction digests of your favorite plasmids. The maps are beautiful and quick to design. It can automatically scan your sequence for relevant genes, and puts them on your plasmid map. You can import VectorNTI, Genebank, EMBL, ApE and FASTA files, and even connect with the NCBI website to do BLAST alignments. I had only 2 problems when trying out the software 1) I could not create a reverse compliment of a sequence I was trying to copy to create a PCR primer and 2) it’s kind of annoying to have to scroll through the list of restriction enzymes. Would be nicer if I could just search for “HindIII” or “EcoR1.” Other than that, it worked great!
ADDENDUM: Dr. Perez reached out to me to clarify the two points of difficulty I had with the software. Regarding point #1 – creating a reverse compliment to a PCR primer – This can easily be done by going to Edit -> Use as reverse PCR primer. Took me a while to find it, but now that I have it will make generating primers easier. Regarding point #2 – search vs. scroll for restriction enzyme names: Dr. Perez pointed out that you can actually start typing and the list will move automatically to the enzyme of interest. However, this only works for the first 3 letters you type unless you’re in the “Sequence Map” window.
I appreciated Dr. Perez’s feedback. He has designed a truly impressive piece of software and it’s wonderful he takes as much pride in it as he does.
That’s it for now. Big props to all the developers out there working to accelerate science by providing free software tools to researchers!