Wednesday, 25 July 2012

SnapGene or the best DNA playing software you'll ever find

Here I am in a marathon of articles to the end of July 2012, and then some very deserved vacations in my home country, Portugal. That, if the Summer fires haven't yet burned the country to ashes or if our Troika friends allow us to breath some air free of taxation. 

Today, I am quite excited about this article, however I won't be fully proficient in explaining every little surprising bit about the software I am here analysing, nonetheless I have used it to a normal extension - PhD wise -, and believe me guys, this software is not only good, it is AWESOME! What am I talking about? Let me tell you a few things first. For all of you who work in molecular biology, specially those that operate plasmids and face the quotidian struggle to rapidly decide what restriction enzyme to use, how does the plasmid map look like, how would a certain digestion look like after a gel run, and a trillion other functions so useful and so necessary that I could take 5 pages to list them all. So to make our long story short I can just present you with a question. What software do you usually use to work out your DNA fragments? The oldest amid you will immediately say that "DNA software is just like these modern DNA kits, in my times we used to do everything by hand and brains". Well, times change, speed up and unfortunately most of us age and are overtaken by progress, so as long as you know in essence what the hell is going on it doesn't really matter if you're using kits, software or magics, you know it, you understand it, full stop. Just embrace progress and use it for your own benefit. And this is when I bring to you the magics of SnapGene. But not only SnapGene, as I also introduce here (for those who are very skeptical) two other software tools for working DNA fragments, GENtle and SimVector. But bare in mind that SnapGene is my very favourite.

I don't intend to make this post way too long, but in honesty I must say I have never been so excited about a software like I am today with SnapGene. Do you know that feeling of total satisfaction when you open up a Xmas gift? Hell yeah!, I feel the same way about SnapGene. Not so much about SimVector, nevertheless I must acknowledge a few good potentialities; and definitely not with GENtle (this one has only one single point where I must admit wins over all the other ones presented here).

Let's then start to look, step-by-step, into the reality of these three software tools:


- SnapGene Viewer allows you to annotate DNA maps and design primers.
- SimVector is an exceptional tool for drawing publication and vector catalog quality plasmid maps, carrying out restriction analysis and designing cloning experiments.
- Gentle is a software for DNA and amino acid editing.


SnapGene Viewer is revolutionary software that allows molecular biologists to create, browse, and share richly annotated DNA sequence files up to 1 Gb in length. It is a great tool for both research and teaching. Here are some of the things you can do with this software. Create a DNA sequence file by either entering a sequence, or importing a record from GenBank, or opening an annotated sequence stored in one of many common file formats. Browse or print a DNA sequence and its annotations using customizable Map, Sequence, Enzymes, Features, Primers, and History views. Search a DNA sequence to match either a DNA query, or a protein translation, or an annotation. Open and edit sequence trace files. Automatically annotate common features, or manually annotate coding sequences and other features. Design and annotate primers for PCR, sequencing, or mutagenesis. Identify open reading frames (ORFs) with a single mouse click. Export a plasmid map as an image, or export an annotated DNA sequence to GenBank format. Freely share data with your colleagues or customers using the universally accessible SnapGene format. [1]
- SimVector 4 allows you to draw Exceptional Publication Quality Plasmid MapsMultiple Cloning Site (MCS) Display is Unique to SimVector, Lightning Fast Cloning Simulation, Restriction Analysis, Biologist-designed Intuitive Interface, Draw Catalog Quality Plasmid Maps, Plan Cloning Experiments, Customize Vector Maps, Printing, Sequence Analysis. [2]
GENtle 1.9.4 is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. [3]

Ranking in Science software:

- SnapGene Viewer is #5. All the others are not even mentioned in the list.


- SnapGene Viewer is all you expect in terms of user-friendly interface. Simple yet deep, interesting yet explanatory, complete yet straightforward.
- SimVector sits right in the middle of the "it could be better" and "sometimes it's not that hard to get it" range.
- GENtle has one of the most uninteresting, complicated and time consuming interfaces I have had to deal with.


SnapGene Viewer is free for 30 days but then you'll have to look down here and find that if your institution is not helping you purchasing it, then it'll be tough for you to put your hands on it.

SimVector 4 can compete with SnapGene in terms of price, but for a student standard is still tough to afford.

GENtle is free. Plain dead simple.

My preferences:

1st) SnapGene Viewer is great; my favourite no doubt, but where in life will I ever have money to get the licensed version?

2nd) SimVector 4 can do a lot and battle in terms of price with the best out there, still for that same reason I'd go SnapGene.

3rd) GENtle, free saves a lot of fuss; but the software is just complicated and ugly for users like me.

Image taken from

[1] GSL Biotech, [], last visited on the 25th of July 2012, last update on the 15th of July 2012.

[2] Premier Biosoft, [], last visited on the 25th of July 2012, last update ounknown.

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