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A Brief Survey of Plasmid Mapping and DNA Annotation Software

Plasmid mapping and DNA annotation software is pretty abundant these days. A quick Google search brings up dozens of hits – but how do you know which one to use?

If you are like most molecular biologists, you probably use the same software your colleagues do—usually it is either the stuff that gets passed down from grad student to grad student or the one licensed software your lab pays for.  Don’t get me wrong—this is not necessarily a bad thing! Many times we don’t go looking for new software because the old stuff suits our needs.

Sometimes though, we don’t want to spend the extra time learning a new program even though it might make our lives easier in the end.

To help get you out of a molecular biology rut, I’m going to introduce you to a few DNA annotation/plasmid mapping programs.  This includes two tried and true favorites, as well as some newer ones that may not have made it onto everyone’s radar yet.

The tried and true favorites:

pDRAW32

Recently updated, pDRAW32 is a free Windows program (but it may be run on a Mac with a porting software such as Wineskin). pDRAW32 is a basic, yet comprehensive, DNA analysis program that can be used for virtual cloning, annotations, and analysis.  It automatically finds restriction sites, methylation sites (dam and dcm), ORFs, and potential primers. For $300 you can purchase a licensed version that eliminates the requirement of regular updating, but the program features are pretty much the same.

ApE

Updated in fall 2012, ApE is free plasmid editor that runs on all three major platforms: Windows, OS X, and Linux.  The program can import DNA Strider, FASTA, Genbank, EMBL and ABI files and exports data in DNA Strider-compatible or Genbank file formats. It has the basic features a molecular biologist is looking for: annotation of sequence, primer and restriction enzyme search, graphic maps, alignments (between two sequences or a sequence and a trace file), and virtual digests.

Some newer players:

Snapgene

SnapGene is versatile software available for Windows and OS X. It combines a lot of great features with a good user interface that allows scientists to plan, visualize, and document cloning and PCR projects.  There are 2 different products: The free SnapGene viewer can make maps and design primers. The licensed version ($345 for a single academic annual license or $695 or a single academic permanent license) provides additional perks such as sequence editing, restriction digest result predictions, and cloning simulations (PCR, Restriction Digests, Gibson, etc). Snapgene is compatible with file formats of many other popular programs such as ApE, Lasergene, Genbank, Vector NTI etc and can import not only the DNA sequences but the annotations, too.

GenBeans

GenBeans is software written in Java to work on Windows, Linux, and Mac. GenBeans is a free molecular biology program for DNA analysis developed by GeneInfinity.  Along with restriction enzyme analysis, it  has primer picking capabilities and a feature that allows you to analyze your oligos to determine melting temperatures, hairpin structures, or dimers. The software allows the user to save and export files in open standard formats (FASTA, Genbank, UniProt, etc) and has an easy to navigate Sequence Feature viewer.

UGene

Ok, so this is not exactly a plasmid mapping or DNA annotation tool, but this free software is quite comprehensive, and looks pretty cool.  If you are looking for a simple cloning or annotation program this one is likely not for you, but for those scientists wanting an all in one program to go from DNA/RNA annotations to 3D structure, this could be a nice tool.  The program works on Windows, Linux and Mac.  Although more user friendly than most bioinformatics tools, it may require a bit of bioinformatics know-how to implement. It incorporates both graphical user and command-line interfaces and the supplied tutorials are a definite help for the less bioinformatics savvy.

If you are in need of DNA annotation programs to perform basic, yet critical functions, (but are not prohibitively expensive) hopefully this list can get you started.

Of course, there are many other great (and maybe not so great) programs out there and I encourage people to comment!

6 Comments

  1. Vladimir on March 22, 2016 at 11:23 pm

    WebDSV is a free DNA annotation/plasmid mapping program running in an internet browser window. As such it is totally cross-platform and requires no installation. It is compatible with the universal GenBank file format. Give it a try!
    http://www.molbiotools.com/WebDSV/index.html

  2. BrantHackett on September 19, 2014 at 3:54 pm

    I can also recommend Gene Construction Kit® (GCK). It’s a useful tool for plasmid mapping, cloning simulation, and DNA analysis. It’s been around since the mid-90’s, and was one of, if not “the very first software” for performing these types of graphical manipulations of DNA sequence data. It has been consistently reviewed (as “idickers” says above) as being one of the easiest to use applications for simulating multi-step cloning operations, and offers extensive flexibility in the graphical formatting of DNA sequences. A free demo version is available from the website, http://www.textco.com. Please check it out!

  3. idickers on December 9, 2013 at 10:17 pm

    I’ve used Gene Construction Kit since the early ’90’s, and really love it. The easiest mapping software I’ve come across.

  4. user-30738 on November 20, 2013 at 3:52 am

    I use Serial Cloner and Geneious pro. Lots of people I know are using Serial Cloner as a free option. I have used Mac vector, Vector NTI, Dnastar, Snapgene and Geneious pro etc. All are good software. Macvector, good but mac only. Vector NTI, used to be free for academic use, no comment. Dnastar (lasergene), too expensive and ugly user interface. Snapgene, very easy to use, the plasmid map in snapgene is just beautiful. Geneious pro, it provides the most complete and powerful solutions. I like the user interface of geneious. Everything is integrated yet it may look a bit sophisticated for some people. I could also use dropbox to synchronize all the database of Geneious pro that I installed in different computers in the lab.

  5. 5 to 16 chars on November 18, 2013 at 10:57 pm

    Serial Cloner is the best free plasmid-mapping software that I’ve come across. For genome browsing (e.g. to find primer-binding sites), Geneious is excellent. It’s not free (as in beer or speech), but it’s reasonably cheap. However, for creating in silico plasmid maps, I still revert to Serial Cloner, which outdoes Geneious in this respect.

  6. Joanne Kamens on November 18, 2013 at 4:30 pm

    We have seen a few Tweets asking us about Benchling (benchling.com). This very new addition to the field and is currently in an “open beta testing” phase. It will be free for personal and academic use after the full launch. Benchling has a nice interface and some nice lab/colleague collaboration features. It may prove to be another good option in this space if it catches on. It is certainly another good one to try out to shake up plasmid and sequence visualization.

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