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10 Things to Look for in Molecular Biology Software

Posted in: Software and Online Tools
molecular biology software

I recently stumbled upon this list of molecular biology software tools. While it is very useful, I thought, “wouldn’t it be easier if ONE program could do many of these tasks!?” Luckily, in the time since that list was published, new software has been developed that does! My favorite, Genome Compiler, is an excellent, free program that encompasses many of the features mentioned in the previous list, and will satisfy most of your molecular biology software needs.

Here are the ten things you should look for when choosing a DNA design program, whether you end up using Genome Compiler or otherwise.

 1.  Cloning Capabilities

This follows the trend of seeking molecular biology software programs that allow you to perform the widest variety of tasks in one place. Look for programs with good cloning tools and a choice of methods with which to clone your sequence. Cloning wizards make the process extremely easy; simply drag and drop your vector and gene of choice in the wizard, and you can visualize the cloning process.

2.  Sequence Annotation

Any good software for designing DNA should allow users to annotate their sequences. It’s great if there is both a manual and auto annotation option so you can choose whichever fits your needs for a specific sequence. Sequence annotation is crucial as a project progresses, so make sure that the software has a simple, organized annotation form. It will make your life much easier down the line.

3.  Primer Design

Every molecular biologist understands the importance of primers for successful DNA amplification. A good software will have features like auto design, cloning, and sequencing primers, as well as a primer library for storing and reusing primers you have previously designed. These libraries allow you to store your primers, keep an updated inventory, easily share with others and automatically attach primers to sequences you’re working on (annealing primers).

4.  File Import

For the times when you’re not starting your project completely from scratch, it’s necessary that a program allows you to import files from elsewhere on the web or saved on your computer. The best programs will let you easily import many different file formats and databases such as NCBI.

5.  Sharing Capabilities

One of the best things about genetic engineering going digital is the ease with which you can collaborate with other researchers. Make sure you choose a program that makes this act simple, with organized libraries that you can easily share with others.

6.  Track Changes

A necessary feature if you plan on editing your sequence as you go (which most researchers do).

7.  Time Saving Tools

Even though molecular biology software makes DNA design much simpler than it used to be, there are still some tasks that can be tedious and time consuming. Look for a software that has embedded emerging technology such as the RBS Calculator to ensure that your design can be completed as quickly and stress-free as possible.

8.  Restriction Enzyme Digest

Virtually running a digest on your sequence and simulating the resulting fragments allows you to judge whether or not your gene is in correct orientation for cloning, avoiding errors and saving you time.

9.  Codon Optimization

Too many codons leads to an oversaturation of ribosomes bound to the mRNA in your system. Make sure the software you choose codon optimizes your design to avoid this “traffic jam” in translation!

10.  Direct Ordering

After your DNA design is finally complete comes the challenge of checking out the synthesis sites and “shopping around”… unless you choose a software that has an ordering feature embedded within it. This is a great perk and a real time saver.

There’s a ton of molecular biology softwares out there, so make sure you do your research to find the designer that has the most features you’ll need all in one place. What’s most important to YOU when choosing a software?

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Image Credit: Nick Page


  1. Sven on August 9, 2018 at 5:20 am

    Hi there,
    i came across a free online and super easy to use PCR primer design tool for cloning projects (Cloning Troll from BioTroll tools). It has a build in multiple cloning site database for the most common expression vectors. Custom ones can be used easily also. The fully automatic tool makes it virtually impossible to create faulty primer sets. It checks for endonuclease sites within the insert and adjusts the reading frame to ensure the correct translation. Plus the entire primer design procedure takes literally seconds! The well structured output summarizes the settings and contains a labeled in silico assembled vector-insert molecule including translation.
    The Cloning Troll tool can be found on :

  2. Julien Dal Col on April 7, 2016 at 4:18 pm

    Benchling is a very good alternative too.

    In my hands it is superior to Genome Compiler, especially in handling data produced using other software.

    Data import is super convenient and fast and auto-annotation as well as auto-primer recognition is super useful especially since we use a shared oligo library and a shared annotation library across the lab.

    People often criticize Benchling because the data is on the cloud. However everything can be exported/downloaded (at once) in just a click. Actually, I download any file I edit and save it on our servers regularly. Then when I don’t need the data in Benchling anymore I delete it from the cloud.


  3. tedus on March 21, 2016 at 7:03 am

    Ugene – Software for genome analysis ( Alternatives: Vector NTI, GenTle, Serial Cloner, pdraw)
    NCBI Genome Workbench – sequence analysis and more
    Jalview – Editor for multiple sequence alignments, Alternative for BioEdit, Artemis

    Also useful when looking for free software are linux distributions in general or specialised: – and also

  4. Pete on March 16, 2016 at 9:09 am

    What’s important to me is that data is not stored “in the cloud” (aka “on someone else’s computer”), the program is “free/libre” [1] and hence safe to use, and cross-platform (i.e. has a native client on Linux). AFAICT Genome Compiler fails on all these points. I’m currently using Geneious and Serial Cloner, neither of which is “free/libre”, but ticks the other boxes. Unfortunately I’m yet to find software that covers all bases.


    • Vladimir on April 6, 2016 at 11:45 am

      Hi, try WebDSV. It is a completely free and platform independent molecular biology software running in a web browser, but with local data processing without any cloud storage. No registration is required and the user stays anonymous. It works with GenBank files so it is compatible with almost any other software. It also allows to edit GenBank file headers including the “comment” field. The user thus can store notes about changes he made directly in sequence files. WebDSV comes accompanied with a bunch of complementary apps for restriction analyses, DNA chemical properties calculations etc.

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