From the first days of unlocking the DNA code, to today synthesizing our own, the past few decades have seen exponential advancements in how we do genetic research. This transformation is owed much to the combination of computer engineering and biology; sister sciences that have become critical partners of genetic research. There are several software platforms that exist today helping molecular biologists and genetic engineers think about and execute their research for grander hypotheses, more immediate results and the production of masses of data. After recently reading the article “Vector NTI Vs Genome Compiler”, let’s continue this comparison with another conventional, widely adopted DNA design platform SnapGene, up against the new kid on the block – Genome Compiler.
With software that allows planning and simulations of DNA manipulations, SnapGene has a good range of scientific add-ons to help molecular biologists and genetic engineers visualize their research. Although relatively new on the scene, Genome Compiler is revolutionising the synthetic biology industry as a one-stop-shop from DNA design, all the way through to ordering sequences straight from the platform.
Familiarization with the SnapGene product comes after studying the handy, but fairly lengthy tutorial videos. For Genome Compiler it seems customer support is paramount with a live chat feature for online round-the-clock support. It was great when I enquired about how to import my alignment files and I received a live instant reply. There are also regular live webinars and short (less than 2 minutes) video tutorials on a range of topics.
Both software packages offer databases populated with thousands of fully annotated plasmids. At this stage, SnapGene supports a greater variety of file formats for importation and their database is more extensive. However, these databases are only accessible on their website so first the files have to be imported from the website in order to view them inside the software, making it less convenient to search for and open projects. By contrast, Genome Compiler has a built-in user-friendly ‘Materials box’, with the ability to search its databases and open projects from within the software platform. Genome Compiler also supports the import of SnapGene files, so if you can’t find the sequence in the Genome Compiler database, you can import files from the databases on the SnapGene website straight into Genome Compiler. Genome Compiler are also integrating plasmid libraries organised according to vendor; they already have the whole of the Addgene and Sigma Aldrich plasmid repositories, with options from within their platform to directly order these plasmids from each vendor. Genome Compiler seems to be constantly expanding the libraries it supports, also having recently added the Synberc plasmid library and the iGEM library of standardised DNA parts.
Cloning ‘wizards’ are included in both software packages to aid step-by-step simulations of a variety of cloning procedures; saving users time and reducing errors in their design. Genome Compiler’s cloning wizards have some additional capabilities, for example allowing you to design primers, add compatible restriction sites where none can be detected in the sequence, or to codon-optimise your synthesized sequences. Additionally, the user can save the cloning wizard steps in case they want to re-open and edit them again at a later date. Currently SnapGene covers a greater variety of cloning procedures (Gateway, In-fusion, Gibson Assembly and TA or GC). But while Genome Compiler already supports Gibson Assembly and Restriction Ligation, it mentions online that Golden Gate and Gateway will be added soon.
One of the advantages of using these computerized systems is to eradicate human error. SnapGene has a really good history-tracking tool, where you can see the whole cloning chain of events that led to your finalized constructed plasmid. Although Genome Compiler doesn’t have this yet, it does provide tracking of the small incremental changes that users make to DNA and amino acid sequences, which are permanently recorded for future reference, and with the ability to note personal comments on the DNA sequence, which is useful for shared projects.
Collaborative work is most definitely encouraged with Genome Compiler’s easy-to-use cloud-sharing facilities with options for both read-only and editing. This is probably the most exciting feature of Genome Compiler in comparison to SnapGene; its usability online, although it can also be downloaded just like SnapGene if you so desire. With no restriction on licences, each user can download the software or use the online version for free; creating their own accounts and working online or offline from their own computers, without the need for sharing one account on one computer. Genome Compiler is ready for use immediately, and from anywhere, and not to mention absolutely free for academia. Genome Compiler can commit to such a structure because of their e-commerce strategy that leverages their corporate partnerships; making money through referrals for DNA purchases at no additional costs to the end user.
So, here we have dissected two software tools that are allowing biologists to imagine, create and share DNA sequences. The technology is only a few years old and both seem to be constantly working to refine their systems with regular updates using crowd-sourced feedback; Genome Compiler appearing the more dynamic of the two with its online functionalities and live chat interactions with users. SnapGene might be the more conventional product with big data storage, but Genome Compiler is the one with a big-picture outlook, differentiating itself with a vision for the entire marketplace; hosting a combined design platform for visualizing, managing data, collaborating and ordering seamlessly from synthesis partners. So go and check out both of these software design tools and decide for yourself, I know which one I have my money on for facilitating the next big discovery leap in the synthetic biology industry.
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April 08, 2014
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