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?