EnzymeX - A plasmid editor for the mackind

While ApE is for the masses, EnzymeX is for classy Mac users. Read on for more...


4Peaks is a pretty well-known piece of program used for work with DNA sequencing trace files. EnzymeX is made by the same guys. Their website has a few other interesting programs for Mac users that are worth trying. EnzymeX is a feature-rich plasmid construct designer and editor. You can download EnzymeX from their website for free. Installation, as with most other Mac softwares, is a simple drag-and-drop of the app into 'Applications' folder.

When opened, the program comes up with three choices: creating a new construct, opening an existing construct, or looking up enzyme information. Using this program, you can design your plasmid construct in silico. If you are designing a protein expression construct, you can translate the insert to make sure the gene insert is in-frame and/or protein sequence is correct.

Going into the details of the program with a full feature list is beyond the scope of this entry. I will however highlight a few things I liked.

• The search box on the top right corner of the main window is fantastic. You can not only search for restriction enzyme sites, but also sequence and sequence motifs (DNA and protein).
  
• 'References' is a nice feature. It has a list of commonly used abbreviations, amino acid structures, codon tables of different organisms, and kozak sequences. In addition, there is a 'buffer composition' table that lists the composition of restriction enzyme buffers bundled with enzymes by different suppliers. If you end up with a sticky end DNA molecule and would like to modify it, 'References' can help you. Just tell the program what you want to do and it will tell you what to do - neat! Finally, the program also lets you visit the ReBase info webpage of any selected restriction enzyme.
  
• 'Calculator' tool is very handy when you have to quickly find out the concentration of particular sample, or convert between micrograms and picomoles, micromolar to picomoles, picomols to ends, etc. Calculator tool also tells you the molecular weight (in kDa) of a particular nucleic acid fragment based on the number of nucletoides; length, molecular weight and estimated Tm of a given oligonucleotide sequence; and given the insert and vector size and concentrations it will even help you set up a ligation reaction!
  
• With EnzymeX, setting up those double digests is very easy. Choose the enzymes and the supplier, this program will tell you which buffers to use. Reaction Mixer will even help you set up the restriction enzyme digestion and lets you print the set up - now that's convenient!
  
• EnzymeX's features are further enhanced by Plugins. I only have a few plugins. One of them allows me to instantly view the hydrophobicity of a translated region of the construct.
  

In my earlier post, I mentioned about a similar program called ApE. While ApE does most of the things EnzymeX does, it lacks the fine interface EnzymeX has. Also, ApE lacks almost all the vendor-specific restriction enzyme features EnzymeX has. I find those features very useful and I am sure anyone who uses a bunch of restriction enzymes (especially from different vendors) routinely will appreciate those features in EnzymeX. One feature that I would like to see in EnzymeX is its ability to open and align ABI chromatogram files with existing constructs (EnzymeX lets you use NCBI BLAST which includes BLAST2Seq). That feature is present in ApE and it is something that I use very frequently. Other features that would be a nice addition to this program include the ability to make nice pictures of plasmids for presentations and publications; ability to design compatible PCR primers, set up PCR reactions much like restriction enzyme digestion reactions, and visualize products in a schematic agarose gel; and ability to design mutagenesis constructs and the primers required for them. In most cases, after plasmid constructs are designed and the genes sub-cloned, attention of the researcher shifts to protein analysis. Addition of useful features for protein analysis like secondary structure prediction from PSIPRED, protein motif recognition, displaying protein parameters as in ProtParam, etc., would make this program even better. It is a pity that this program is available only for Mac users. It would be excellent to have this program available for Microsoft Windows and GNU/Linux users also (I have a MacBook, two computers running Kubuntu and I share a lot of constructs with Microsoft Windows users). I would like to congratulate Mek and Tosj for such a wonderful job creating EnzymeX and thank them for providing it for free.
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A Plasmid Editor

I am a biochemist. And as almost every biochemist these days, I do some sub cloning. Working with all those DNA and/or protein sequences can sometimes be confusing. I always wanted a small program that can help me organize those sequences. So, one fine day, I set out on a search for that perfect program. Some of my criteria were:

• Interoperability I use a Mac Book. My home computer runs on Linux and about a dozen computers in my lab run Windows. So, I am looking for a program that can be run on all three platforms.

• Free Plain and simple. I don't want to pay any money!

• Simple and Intuitive I do not want to spend a lot of time figuring out how to use the program. I want to get on with my work, right away.

After some googling, I found this program called ApE. ApE stands for A plasmid Editor. ApE is available for download here. It can be run on Windows/Linux/Mac. I won't go through the features; but one can pretty much do all steps of sub cloning (on the computer) using this program. It has a nice intuitive interface. Although the program comes with a .doc documentation file, I never had to even look into it to use it! The author says this would be the last release of this program; so that could be an issue. Anyhow, I like this program even in its present form - there aren't any features I feel it should have and I did not encounter any bugs.
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