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Battle of the Bargains: A Comparison Between Genome Compiler and ApE

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Synthetic biology software should make your life easier. Unfortunately, choosing the wrong software platform to work with can lead to problems down the line, and finding the best program for your needs can be a complicated process.

Similar to the article comparing Genome Compiler and Snapgene, I’m going to compare Genome Compiler with ApE, to look at another option. This comparison should help you decide which software is the best for your needs.

User Experience/User Interface

Upon first opening ApE, I felt overwhelmed. The blank, stark program is not very user friendly or inviting to begin a project on. The action icons at the top of the screen are not labeled, requiring the user to hover over the icons simply to know where to begin.

By contrast, Genome Compiler is extremely user friendly from the get-go, on both the desktop and browser versions. Unlike ApE’s blank screen, Genome Compiler prompts users with different types of projects to begin and various file import options. This friendly interface makes it very easy to get to work right away. Another great aspect of the Genome Compiler interface is the materials box, displayed prominently on the home screen. It is very easy to choose a file from the list of sequences, which includes both your own files and those provided in the Genome Compiler library. ApE does have an inventory of enzymes to choose from, but no sequence library, and finding the enzyme selector is a bit more complicated.


Of course, one of the key things to check out about any potential program you’re going to use is price. But, it’s not an issue in this case – both Genome Compiler and ApE are completely free. Given that licenses for other programs can run over a thousand dollars, this is a huge plus for both of these tools.

Operating System Compatibility

In addition to price, compatibility is one of the most important, basic factors that goes into deciding which software to use. Both Genome Compiler and ApE are Windows and Mac compatible, and ApE is also Linux compatible. In addition to the downloadable desktop program, Genome Compiler is also available in an online version, which makes it easy to work from anywhere without needing to install any software on to a computer.

File Format Support

Along with computer compatibility, you need to look at what file formats a software supports. ApE can import DNA strider, Fasta, Genbank, GCG, EditSeq, and EMBL files. Genome Compiler can import files from the most commonly used biology software tools and, furthermore, the range of accepted formats continues to grow. Thus, it is more likely that your desired sequence will open in Genome Compiler than ApE.


Both Genome Compiler and ApE offer sequence annotation and alignment, primer design, ORF detection, and gel simulation. However, the annotation and alignment features on ApE are manual, whereas Genome Compiler has wizards that can complete these tasks automatically. Additionally, I find the sequence view in ApE too compact, making it difficult to actually read the sequence you’re working on.

Genome Compiler also has special features including the RBS Calculator, and wizards for Gibson assembly and restriction ligation to auto generate oligos, primers, and simulated assemblies of the final cloned products. On ApE, you must copy and paste sequences to assemble them. You can also easily tag your projects on Genome Compiler, which is great for organization purposes. Overall, you can do more, and complete tasks with more ease and less stress, on Genome Compiler than ApE.

Customer Support

While ApE has a Wiki page for users to submit questions, the customer support more or less ends there. Other than the Wiki page, I was able to find a few short tutorial videos put on YouTube by a user not affiliated with ApE. Meanwhile, Genome Compiler has a plethora of tutorials and longer webinars giving in-depth explanations of how to use the software and its features. Additionally, you can submit questions to a Genome Compiler representative at any time via their live chat tool in the software and receive real-time help as you’re working inside the program. Even with the Wiki questions and answers page, a little more guidance would go a long way for first time users of ApE.

Data Storage and Management

Saving your files on ApE entails simply saving it to your computer. Along with basic local saving, Genome Compiler is equipped with a cloud based tool. By saving your work to the secure cloud, your sequences essentially become portable and you can access them by logging into your account at anytime, from anywhere. In addition to the previously mentioned materials box and sequence library, Genome Compiler also has a primer library. Users can import primers into their library and then easily share these libraries with colleagues. This tool allows researchers to efficiently manage the lab’s sequences, primers, and parts, and means you won’t waste time redesigning or reordering the same primers.

Data Sharing

As mentioned above, Genome Compiler users have access to the platform-secured cloud. The cloud allows users to easily share their folders of data with colleagues. It’s a simple process of right clicking on the folder, selecting “share” and then entering the collaborators email addresses. Multiple users then have access to the data, and it’s even possible to track each other’s changes on the shared data and view the editing history. On the contrary, ApE users must use the traditional methods of Google drive, Dropbox, flash drives, email or the like to share their work with colleagues. The Genome Compiler cloud greatly improves the process by eliminating the need to use any of these tools.


Clearly, if you’re looking for a free software that offers you the widest array of features, Genome Compiler is the way to go. Overall, Genome Compiler’s features are less labor and time intensive for users than ApE. And, the excellent tutorial videos and customer support by Genome Compiler means you’ll save time learning the software and figuring out any issues you may encounter.

While you can’t go wrong trying out any program with a free price tag, you’ll get more for your hypothetical buck with Genome Compiler than ApE.

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  1. Alejandro on March 10, 2016 at 7:39 pm

    @Robin: You can use the web version of GC with no installation. For the desktop version you will need the Adobe Integrated Runtime so yes, in that case you’ll need a green light from IT.

  2. Robin Gort on February 23, 2016 at 12:51 pm

    Will Gene Compiler work without an installation required? ApE saves the hassle of having to pass an IT department.

  3. Niek on February 23, 2016 at 11:24 am

    btw, there is actually a wizard for genome annotation in ApE. (Features –> annotate features using library).
    That being said, I prefer genome compiler over ApE.

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