Create a Pairwise DNA Alignment

How do I create a pairwise DNA alignment?

The SnapGene pairwise alignment tool uses Parasail to align and compare two DNA and/or RNA sequences.

Parasail provides three alignment methods:

  • Local Alignment
  • Global Alignment
  • Semi-Global alignment

Click Tools → Align Sequences → Summary of Alignment Algorithms to learn about  Parasail.

Note that the pairwise alignment tool does not check or automatically flip nucleotide sequences so that all are in the appropriate orientation. You should examine each sequence to confirm orientation, flip a sequence if required, then perform the alignment.

Option 1: Start with a Collection

Create or open a SnapGene Collection.

Selection two sequences from the Collection as input for alignment.

Click Tools → Align Sequences → Align two DNA sequences.

The selected sequences will be automatically entered as input for pairwise alignment.

Option 2: Start with Individual Files

Click Tools → Align Sequences → Align Two DNA Sequences....

Set the two sequences for alignment, use any combination of the following methods to add each sequence:

  • Paste DNA sequences into the fields provided
  • Drag individual sequence files into the fields provided
  • Click Please Choose and select a "Recent DNA file"
  • Click Please Choose → Browse to specify a sequence located somewhere on your computer
  • Click the Import button to import a sequence from NCBI (using an accession number)

Set the algorithm or algorithms to use for pairwise alignment.

SnapGene provides three pairwise alignment algorithms.

Click menu Tools → Align Sequences → Summary of Alignment Algorithms to learn more about each pairwise algorithm.

Once sequences and alignment algorithms are defined, edit the sequence names if required (these names will be displayed in the alignment) then click Align to create an alignment file.

View the Alignment

If more than one alignment algorithm was selected then use the "Aligned using" dropdown to view each alignment.

Configure how differences between the sequences are displayed using the "Format" drop-down in the side panel.

View the "Side Panel" to view key information about the alignment.

If required, add a description of the alignment in the side panel.

Save the Alignment

Click Save to save the alignment to an appropriate location on your computer.