Create a Pairwise Protein Alignment

How do I create a pairwise protein alignment?

The SnapGene pairwise alignment tool uses Parasail to align and compare two protein 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.

Option 1: Start with a Collection

Create or open a SnapGene Collection that contains protein sequences of interest.

Selection two protein sequences in the Collection as input for alignment.

To start the alignment, simply click the "Align Selected Sequences" button in the Collection window, or alternatively, click Tools → Align Sequences → Align two DNA sequences.

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

Option 2: Start with Individual Files

Click Tools → Align Sequences → Align Two Protein Sequences....

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

  • Paste protein sequences into the fields provided
  • Drag individual sequence files into the fields provided
  • Click Please Choose and select a "Recent Protein file"
  • Click Please Choose → Browse to specify a sequence located somewhere on your computer
  • Click the Import button to import a sequence from NCBI or Uniprot (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), name 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.

Click a disclosure triangle to view features associated with a sequence and see a number line.

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.