Annotate and Visualize
Course Content
Working With Predicted ORFs
Working with Features
Create Primers and Simulate PCR
Silent Mutations: Remove a Restriction Site
View RNA Secondary Structures in SnapGene
Common Questions About Using SnapGene
Can SnapGene automatically annotate features on a new sequence?
Yes. When you import or paste a sequence, SnapGene searches it against a curated library of common plasmid features and automatically annotates matches. You can also save custom features and apply them to future sequences.
How does SnapGene detect open reading frames?
SnapGene visualizes predicted ORFs across all six reading frames directly on the sequence map. You can identify coding regions, check frame orientation, and convert a predicted ORF into a translated (CDS) feature within the same view.
Can SnapGene remove a restriction enzyme site without altering the protein sequence?
Yes. The silent mutation tool identifies synonymous codon substitutions that eliminate a restriction site while preserving the amino acid sequence. The target site must lie within a translated (CDS) feature. SnapGene shows which alternative codons are viable, greys out those that will not remove the site, and displays the unchanged translation alongside the proposed nucleotide change. You can then either mutate the sequence directly or have SnapGene design mutagenic primers and simulate PCR-based mutagenesis.
Does SnapGene support RNA secondary structure prediction?
Yes. SnapGene uses the ViennaRNA package to predict secondary structure for single-stranded RNA and DNA sequences up to 3,000 nucleotides in length. The predicted structure is displayed with confidence coloring indicating the probability of each base being paired or unpaired.
Can I design primers and simulate PCR within the same file?
Yes. Primers can be created manually, imported from a delimited list, or automatically designed in SnapGene. Once primers are added, you can simulate a PCR reaction directly against your sequence and view the predicted product, all within the same .dna file.
What is the difference between this video series and the Working with Primers series?
This series covers the broader annotation and visualization toolset, including ORF detection, feature editing, silent mutations, RNA structure prediction, and primer basics. The Working with Primers series delves deeper into primer-specific workflows, including primer design with 5' extensions, directed mutagenesis, and primer export for ordering.
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