#SNAPGENE VIEWER TUTORIAL HOW TO#
#SNAPGENE VIEWER TUTORIAL FULL#

This vector is available in SnapGene's list of fluorescent protein genes and plasmids. On the webpage of pAcGFP1-C1 click pAcGFP1-C1.dna: Try to load it without peeking at the solution. Loading vector sequences from other resources Go back to SnapGene and click the Open button in the top menu:īrowse to the pAcGFP1-C1.dna file and open it. However, not all vector sequences are stored in the SnapGene database. In SnapGene you can load sequences directly from Genbank or you can load them by importing a file.įortunately, many vectors are available from Addgene, an organization that improves sharing of plasmids. Even if you don't load them from Genbank it is still a good idea to import them in Genbank format (and not in Fasta format). Genbank format not only contains a sequence but also all annotations. If you load the annotations (in Genbank format) SnapGene will automatically show them.

#SNAPGENE VIEWER TUTORIAL FULL#

On the next page containing the full sequence of the vector, click the Analyze Sequence button on the right: On the webpage of mRFP-Rab5 go to the SEQUENCE INFORMATION section and click Full (1) next to Depositor Sequences: Obtain the annotated sequence of mRFP-Rab5 from Addgenes. On the next page select the Sequence tab: SNAPGENE VIEWER NOT OPENING FULL To include the annotation, you need the sequence in Genbank format:Ĭopy the text and paste it in Notepad. Open the annotated sequence of mRFP-Rab5 in SnapGene.Ĭlick the Open button in the top menu, browse to the mRFPrab5.txt file and open it. Rab5 from position 1330 to position 1977.mRFP1 from position 613 to position 1329.We are going to correct the annotation: change the names of the ORFs and split ORF frame 1 into two parts: what is called ORF frame 1 in the map is a fusion between mRFP1 (a red fluorescent protein) and human Rab5 (a small GTPase that is a key regulator of intracellular membrane trafficking) gene.what is called ORF frame 2 in the map is a neomycin/kanamycin resistance gene.Since it's a vector sequence, select circular:Ĭlick OK to open the sequence in SnapGene.Ĭhanging annotation of sequences in SnapGeneĪlthough we imported mRFP1-Rab5 in Genbank format, the annotation that was included in the file was not complete: SnapGene will ask you wether the sequence is linear or circular. To switch back to mRFPrab5 click Window in the top menu and select mRFPrab5. Right click ORF frame 2 in the map and select Edit Feature:Ĭhange name of the feature in NeoR/KanR and click OK:Ĭhange the name of ORF frame 1 and annotate it as a fusion.

Change name of the feature in mRFP1-Rab5įill in the names, start and stop positions of the two genes and click OK.

#SNAPGENE VIEWER TUTORIAL HOW TO#

See the introduction tutorial video and the working with features tutorial video for further details on how to annotate sequences in SnapGene.

Go to the Changing what you see in SnapGene tutorial to see how you can switch between views, change a view, show additional info. SnapGene is not the ideal tool for designing primers. Go to the Primer design in SnapGene tutorial to see how you can use SnapGene to design primers Primer specificity: the ability of a primer to bind to a single or to multiple regions in the genome It does not take into account the ability of primers to form hairpins or dimers nor does it check the specificity of the primers.

So only when you have no flexibility in your choice of primers, I would use SnapGene to design them. This is often the case in cloning experiments when the primer has to be located at the start of the coding sequence.

Simulate PCR in SnapGene Create the product that would be generated when doing PCR with the primers.Įxpand Actions in the top menu and select PCR If you want to design primers for other applications where efficiency and specificity of the primers has to be taken into account, you shouldn't use SnapGene, use CLC Main Workbench or Primer-Blast instead. The primers that you selected are now shown in purple on the map. Click the forward primer and shift click the reverse primer (red).Give the PCR product an informative name e.g.AmplifiedRab5 (green)Įxercise: generate a PCR product of the AcGFP1 gene To clone the fusion into the pCDNA3 vector we need a HindIII restriction site at the 5' end of AcGFP1.

Snapgene viewer tutorial