The program is able to read all files within that folder and you can perform actions on the collection (e.g. Support for collections: A collection is simply a folder with SnapGene files.However, I can see that this would be useful for wet lab scientists who quickly want to get some work done without spending hours on writing a Biopython script or learning the syntax of EMBOSS commands. For me, this feature is not essential since I do most of my protein sequence work with BioPython or EMBOSS. SnapGene focuses on implementing features fast and the documentation often lags behind. Support for protein sequences: This is still experimental and many options are grayed out (at least on my version).I tried it out and it's fairly easy to deploy. If you want to publish your constructs online, this would be a nice way to go. Since I last wrote about the SnapGene software ( ), many good things have happened: Right click the figure and select Export History.Snapgene is a software for the wet lab molecular biologist, who does lots of cloning work (construct design and annotation). This visual representation of the cloning process is very informative and could be used in publications. Go to the pcDNA4_TO_Rab5 sequence: this is the product generated by cloning the Rab5 gene in the pCDNA4_TO vectorĬlicking the History tab in the view shows how this sequence was generated: When you click the Clone button (green) you generate the product. At the bottom of the window you see an overview of the cloning strategy. Go back to the page of the vector where both enzymes are still selected and click the Paste button (red) in the top toolbar: The sites and the selected fragment should be colored blue upon selection. This defines the fragment that is to be inserted during the cloning. Select both enzymes in the map view of the amplified Rab5 fragment by holding the Shift key during selection. Generate the fragment you are going to use. The sites and the fragment should be colored blue upon selection. This defines the fragment that is to be replaced during the cloning. Select both enzymes in the circular view of the vector by holding the Shift key during selection. Indicate the restriction sites that you are going to use. Once you know the enzymes you are going to use you can simulate the cloning. If you want to change this Expand Enzymes in the top menu and select Use Enzyme Set and select Unique Cutters to include enzymes that bind once but have a smaller restriction site or Unique & Dual Cutters (red) to include enzymes that bind twice in the sequence:Īs far as we know, SnapGene does not allow to select on overhang type as CLC does. SnapGene shows by default only cutters that cut only once in the sequence and that have a restriction site of at least 6nt (red). Go to the BamHI page: there you'll see a lot of useful info on the use of the enzyme together with a list of enzymes with the same restriction site (red) if there are any and a list of enzymes generating compatible sticky ends (green).Ĭheck which enzymes cut only once in the Rab5 PCR product This opens the Restriction Enzymes window. finding compatible enzymesĬheck which enzymes generate sticky ends that are compatible with BamHIĮxpand Enzymes in the top menu and select Restriction Enzymes (red): It has useful features some of them are not avaliable in CLC e.g. SnapGene can help you choosing the appropriate enzymes. You can see the ends that are created by these enzymes by hovering your mouse over their name: Which overhangs are created by these enzymes ? To this end we want to use restriction enzymes from the multiple cloning site in the vector that cut in the primers but not in the gene of interest.įind two enzymes from the multiple cloning site in the vector that cut in the primers but not in the Rab5 gene.īy looking at the enzymes we can see that BspE1 and BamHI cut in the multi-cloning site of the vector and in the primers but not in the Rab5 gene. We want to clone the amplified Rab5 fragment in the vector. We go back to the pcDNA4/TO vector: as you can see restriction sites are automatically visualized in SnapGene: 1.1 More on restriction analysis in SnapGene.1 Finding restriction sites in the vector.
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