How do I map peptides to a protein sequence?

The mappers in Geneious Prime will only work with DNA sequences.

You can map peptides to a reference protein sequence using multiple alignment with non-standard settings as follows:

1.  Select all of your peptides and your reference protein sequence.

2. Go Align/Assemble -> Multiple Alignment.

3. Choose the Geneious Alignment tool, click More/Fewer Options and set Gap extension penalty to 0 and Refinement Iterations to at least 3.
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Click OK and the peptides should align correctly to the reference protein.

4. Select the new alignment, right-click on the reference sequence and choose Set as reference sequence. The reference will be highlighted yellow.

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5. If required, click and drag the Name of the Reference sequence to move it to the top of the alignment. 

6. Right click on any sequence in the alignment and choose Sort -> By Position to order all peptides sequentially based on their start coordinate.

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Save. You should now have the equivalent of a map to reference assembly of peptides to a protein sequence. By default, the consensus sequence will be based on the peptide sequences only.

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